WorldWideScience

Sample records for genome referenced intron-flanking

  1. Referencing academic assignments.

    Science.gov (United States)

    Gopee, N

    External examiners often identify inaccurate referencing as a weakness in scripts submitted for assessment. This article explores the main aspects of referencing, and offers a protocol for referencing founded on the Harvard (name-date) system.

  2. The Unusual 23S rRNA Gene of Coxiella burnetii: Two Self-Splicing Group I Introns Flank a 34-Base-Pair Exon, and One Element Lacks the Canonical ΩG▿

    Science.gov (United States)

    Raghavan, Rahul; Miller, Scott R.; Hicks, Linda D.; Minnick, Michael F.

    2007-01-01

    We describe the presence and characteristics of two self-splicing group I introns in the sole 23S rRNA gene of Coxiella burnetii. The two group I introns, Cbu.L1917 and Cbu.L1951, are inserted at sites 1917 and 1951 (Escherichia coli numbering), respectively, in the 23S rRNA gene of C. burnetii. Both introns were found to be self-splicing in vivo and in vitro even though the terminal nucleotide of Cbu.L1917 is adenine and not the canonical conserved guanine, termed ΩG, found in Cbu.L1951 and all other group I introns described to date. Predicted secondary structures for both introns were constructed and revealed that Cbu.L1917 and Cbu.L1951 were group IB2 and group IA3 introns, respectively. We analyzed strains belonging to eight genomic groups of C. burnetii to determine sequence variation and the presence or absence of the elements and found both introns to be highly conserved (≥99%) among them. Although phylogenetic analysis did not identify the specific identities of donors, it indicates that the introns were likely acquired independently; Cbu.L1917 was acquired from other bacteria like Thermotoga subterranea and Cbu.L1951 from lower eukaryotes like Acanthamoeba castellanii. We also confirmed the fragmented nature of mature 23S rRNA in C. burnetii due to the presence of an intervening sequence. The presence of three selfish elements in C. burnetii's 23S rRNA gene is very unusual for an obligate intracellular bacterium and suggests a recent shift to its current lifestyle from a previous niche with greater opportunities for lateral gene transfer. PMID:17644584

  3. Assessing Student Understanding of the "New Biology": Development and Evaluation of a Criterion-Referenced Genomics and Bioinformatics Assessment

    Science.gov (United States)

    Campbell, Chad Edward

    Over the past decade, hundreds of studies have introduced genomics and bioinformatics (GB) curricula and laboratory activities at the undergraduate level. While these publications have facilitated the teaching and learning of cutting-edge content, there has yet to be an evaluation of these assessment tools to determine if they are meeting the quality control benchmarks set forth by the educational research community. An analysis of these assessment tools indicated that valid and reliable inferences about student learning. To remedy this situation the development of a robust GB assessment aligned with the quality control benchmarks was undertaken in order to ensure evidence-based evaluation of student learning outcomes. Content validity is a central piece of construct validity, and it must be used to guide instrument and item development. This study reports on: (1) the correspondence of content validity evidence gathered from independent sources; (2) the process of item development using this evidence; (3) the results from a pilot administration of the assessment; (4) the subsequent modification of the assessment based on the pilot administration results and; (5) the results from the second administration of the assessment. Twenty-nine different subtopics within GB (Appendix B: Genomics and Bioinformatics Expert Survey) were developed based on preliminary GB textbook analyses. These subtopics were analyzed using two methods designed to gather content validity evidence: (1) a survey of GB experts (n=61) and (2) a detailed content analyses of GB textbooks (n=6). By including only the subtopics that were shown to have robust support across these sources, 22 GB subtopics were established for inclusion in the assessment. An expert panel subsequently developed, evaluated, and revised two multiple-choice items to align with each of the 22 subtopics, producing a final item pool of 44 items. These items were piloted with student samples of varying content exposure levels

  4. Academic Practice, APA Referencing Style

    DEFF Research Database (Denmark)

    Nielsen, Sandro; Heine, Carmen

    kildeangivelse og referencer i henhold til APA referencing system.Vejledning i at undgå plagiering ved at følge de normer, der gælder for good academic practice. Dette indebærer at man angiver kilder korrekt, og når det er nødvendigt, og at man har en korrekt udformet fortegnelse over referencer. Vejledningen...... indeholder konkrete eksempler på korrekt kildeangivelse og referencer i henhold til APA referencing system....

  5. Referencing handbook: OSCOLA

    OpenAIRE

    Williams, Helen

    2016-01-01

    University of Lincoln approved guide to OSCOLA referencing. Providing guidelines on how to reference UK, EU and International primary sources of law and secondary sources. The handbook provides examples and annotated diagrams to help you reference sources in the OSCOLA style.

  6. Referencing handbook: Harvard

    OpenAIRE

    Elkin, Judith; Ortega, Marishona; Williams, Helen

    2016-01-01

    University of Lincoln approved guide to Harvard referencing. Providing guidelines on how to reference 75 sources of information. The second edition includes extended guidance on how to reference, all new examples, additional annotated diagrams and an index to help you locate sources.

  7. Selectivity in Infant Social Referencing

    Science.gov (United States)

    Stenberg, Gunilla

    2009-01-01

    In laboratory studies of social referencing, infants as young as 12 months have been reported to prefer looking at the experimenter over the caregiver for clarifying information. From an expertise perspective, such behavior could be interpreted as if the infant seeks information from others and can discriminate between persons who have or do not…

  8. Intronic alternative splicing regulators identified by comparative genomics in nematodes.

    Directory of Open Access Journals (Sweden)

    Jennifer L Kabat

    2006-07-01

    Full Text Available Many alternative splicing events are regulated by pentameric and hexameric intronic sequences that serve as binding sites for splicing regulatory factors. We hypothesized that intronic elements that regulate alternative splicing are under selective pressure for evolutionary conservation. Using a Wobble Aware Bulk Aligner genomic alignment of Caenorhabditis elegans and Caenorhabditis briggsae, we identified 147 alternatively spliced cassette exons that exhibit short regions of high nucleotide conservation in the introns flanking the alternative exon. In vivo experiments on the alternatively spliced let-2 gene confirm that these conserved regions can be important for alternative splicing regulation. Conserved intronic element sequences were collected into a dataset and the occurrence of each pentamer and hexamer motif was counted. We compared the frequency of pentamers and hexamers in the conserved intronic elements to a dataset of all C. elegans intron sequences in order to identify short intronic motifs that are more likely to be associated with alternative splicing. High-scoring motifs were examined for upstream or downstream preferences in introns surrounding alternative exons. Many of the high-scoring nematode pentamer and hexamer motifs correspond to known mammalian splicing regulatory sequences, such as (TGCATG, indicating that the mechanism of alternative splicing regulation is well conserved in metazoans. A comparison of the analysis of the conserved intronic elements, and analysis of the entire introns flanking these same exons, reveals that focusing on intronic conservation can increase the sensitivity of detecting putative splicing regulatory motifs. This approach also identified novel sequences whose role in splicing is under investigation and has allowed us to take a step forward in defining a catalog of splicing regulatory elements for an organism. In vivo experiments confirm that one novel high-scoring sequence from our analysis

  9. Referencer

    DEFF Research Database (Denmark)

    Wille, Niels Erik

    , APA, CSE og ISBD, samt den nyeste udgave af den danske/internationale standard på området (DS/ISO 690:2010). Diskuterer de såkaldte "Harvard"-regler som ikke er et entydigt system, men en række varianter over henvisninger af typen Navn+Årstal. Målgruppe: Specialestuderende, ph.d.-studerende og...

  10. Memory for details with self-referencing.

    Science.gov (United States)

    Serbun, Sarah J; Shih, Joanne Y; Gutchess, Angela H

    2011-11-01

    Self-referencing benefits item memory, but little is known about the ways in which referencing the self affects memory for details. Experiment 1 assessed whether the effects of self-referencing operate only at the item, or general, level or whether they also enhance memory for specific visual details of objects. Participants incidentally encoded objects by making judgements in reference to the self, a close other (one's mother), or a familiar other (Bill Clinton). Results indicate that referencing the self or a close other enhances both specific and general memory. Experiments 2 and 3 assessed verbal memory for source in a task that relied on distinguishing between different mental operations (internal sources). The results indicate that self-referencing disproportionately enhances source memory, relative to conditions referencing other people, semantic, or perceptual information. We conclude that self-referencing not only enhances specific memory for both visual and verbal information, but can also disproportionately improve memory for specific internal source details.

  11. Cross-Referencing the Lab Manuals.

    Science.gov (United States)

    Roeder, John L.

    1984-01-01

    Presents a table cross-referencing 12 physics laboratory manuals by topics. Topic areas include measurement and techniques, mechanics, molecular physics, waves and optics, electricity and magnetism, and quantum physics. (JN)

  12. Dogs' Social Referencing towards Owners and Strangers

    OpenAIRE

    Merola, Isabella; Prato-Previde, Emanuela; Marshall-Pescini, Sarah

    2012-01-01

    Social referencing is a process whereby an individual uses the emotional information provided by an informant about a novel object/stimulus to guide his/her own future behaviour towards it. In this study adult dogs were tested in a social referencing paradigm involving a potentially scary object with either their owner or a stranger acting as the informant and delivering either a positive or negative emotional message. The aim was to evaluate the influence of the informant's identity on the d...

  13. Citing & Referencing Using the Harvard Style: Examples

    OpenAIRE

    Cullen, John G.

    2016-01-01

    This teaching resource supplements 2 videos which are available online on YouTube. These videos are titled: • ‘Citing and referencing using the Harvard Style (Part 1)’ - Available at https://www.youtube.com/watch?v=9X1UjtfgTU8 • Citing and referencing using the Harvard Style (Part 2)’ - Available at https://www.youtube.com/watch?v=Hj_EXIFviZA

  14. The Cross-Referenced Patent Cooperation Treaty

    NARCIS (Netherlands)

    Mulder, C.A.M.

    2009-01-01

    'The Cross-Referenced Patent Cooperation Treaty' is a book covering the 'Patent Cooperation Treaty (PCT)' and the 'Regulations under the PCT'. The large number of references in the articles and rules makes the PCT difficult to read. The idea behind this book is to add cross-references to the

  15. The Cross-Referenced Patent Cooperation Treaty

    NARCIS (Netherlands)

    Mulder, C.A.M.

    2012-01-01

    'The Cross-Referenced Patent Cooperation Treaty' is a book covering the 'Patent Cooperation Treaty (PCT)' and the 'Regulations under the PCT'. The large number of references in the articles and rules makes the PCT difficult to read. The idea behind this book is to add cross-references to the

  16. The Cross-Referenced Patent Cooperation Treaty

    NARCIS (Netherlands)

    Mulder, C.A.M.

    2015-01-01

    'The Cross-Referenced Patent Cooperation Treaty' is a book covering the 'Patent Cooperation Treaty (PCT)' and the 'Regulations under the PCT'. The large number of references in the articles and rules makes the PCT difficult to read. The idea behind this book is to add cross-references to the

  17. The Cross-Referenced Patent Cooperation Treaty

    NARCIS (Netherlands)

    Mulder, C.A.M.

    2013-01-01

    'The Cross-Referenced Patent Cooperation Treaty' is a book covering the 'Patent Cooperation Treaty (PCT)' and the 'Regulations under the PCT'. The large number of references in the articles and rules makes the PCT difficult to read. The idea behind this book is to add cross-references to the

  18. The cross-Referenced Patent Cooperation Treaty

    NARCIS (Netherlands)

    Mulder, C.A.M.

    2014-01-01

    'The Cross-Referenced Patent Cooperation Treaty' is a book covering the 'Patent Cooperation Treaty (PCT)' and the 'Regulations under the PCT'. The large number of references in the articles and rules makes the PCT difficult to read. The idea behind this book is to add cross-references to the

  19. User Defined Geo-referenced Information

    DEFF Research Database (Denmark)

    Konstantas, Dimitri; Villalba, Alfredo; di Marzo Serugendo, Giovanna

    2009-01-01

    . In this paper we present two novel mobile and wireless collaborative services and concepts, the Hovering Information, a mobile, geo-referenced content information management system, and the QoS Information service, providing user observed end-to-end infrastructure geo-related QoS information....

  20. Geo-Referenced Health Information for Maternal and Child Health ...

    International Development Research Centre (IDRC) Digital Library (Canada)

    referenced health facility information can inform maternal and child health service planning and decision-making in Bangladesh. Geo-referenced data associates information with a physical space or location. This information can improve data ...

  1. A guide to the Harvard referencing system.

    Science.gov (United States)

    Dwyer, M

    This article explains how to reference an academic work using the Harvard system. Instructions comply with the relevant British standards, i.e. BS 5605:1990, BS 1629:1989 and BS 6371:1983. The importance of referencing in an approved manner is discussed and problem areas such as joint authors, corporate authorship and unpublished works are examined. The issue of second-hand references that are not addressed by the standards is also explained.

  2. Data mining for multiwavelength cross-referencing

    Science.gov (United States)

    Voisin, Bruno; Donas, Jose

    2001-11-01

    In this paper, we deal with FOCA ultraviolet data and their cross-referencing with the DPOSS optical catalog, through data mining techniques. While traditional cross-referencing consists in correcting catalog coordinates in order to seek nearest candidate, non-optical surveys tend to have lower resolutions and more coordinates uncertainties. Then, it seemed to be a loss not to use more light sources parameters obtained through image processing pipelines. A data mining approach based on decision trees (machine learning algorithms), we processed different FOCA/DPOSS sources pairs that we could suppose being the same stellar entity, and some other pairs, obviously too distant to match. Trees use every existing ultraviolet/optical parameter present on catalog, excluding only coordinates. The resulting trees allows a classification of any FOCA/DPOSS pair, giving a probability for the pair to match, i.e. come from the same source. The originality of this method is the use of non-position parameters, that can be used for cross-referencing various catalogs in different wavelength without the need to homogenize coordinates systems. Such methods could be tools for working on upcoming multi-wavelength catalogs.

  3. Collaborative Referencing between Individuals with Aphasia and Routine Communication Partners.

    Science.gov (United States)

    Hengst, Julie A.

    2003-01-01

    This study examined how four adults with aphasia collaborated with routine communication partners. Overall, these pairs completed the referencing task trials with accuracy and displayed referencing processes that conformed to the collaborative referencing model of communication. However, the pairs also used diverse verbal and nonverbal resources,…

  4. Psychoanalytic theory and loving God concepts: parent referencing versus self-referencing.

    Science.gov (United States)

    Buri, J R; Mueller, R A

    1993-01-01

    We investigated the relationship of college students' conceptions of the wrathfulness-kindliness of God to their parents' nurturance, their parents' permissiveness, authoritarianism, and authoritativeness, and the students' own self-esteem. Although parents' nurturance, authoritarianism, and authoritativeness were related to participants' conceptions of God (thus providing some support for psychoanalytic assertions), the variable of self-esteem far outweighed all other variables in accounting for the variance in God concepts. These results suggest that self-referencing explanations better account for individuals' conceptions of God than do parent referencing (i.e., psychoanalytic) explanations.

  5. Dogs' social referencing towards owners and strangers.

    Directory of Open Access Journals (Sweden)

    Isabella Merola

    Full Text Available Social referencing is a process whereby an individual uses the emotional information provided by an informant about a novel object/stimulus to guide his/her own future behaviour towards it. In this study adult dogs were tested in a social referencing paradigm involving a potentially scary object with either their owner or a stranger acting as the informant and delivering either a positive or negative emotional message. The aim was to evaluate the influence of the informant's identity on the dogs' referential looking behaviour and behavioural regulation when the message was delivered using only vocal and facial emotional expressions. Results show that most dogs looked referentially at the informant, regardless of his/her identity. Furthermore, when the owner acted as the informant dogs that received a positive emotional message changed their behaviour, looking at him/her more often and spending more time approaching the object and close to it; conversely, dogs that were given a negative message took longer to approach the object and to interact with it. Fewer differences in the dog's behaviour emerged when the informant was the stranger, suggesting that the dog-informant relationship may influence the dog's behavioural regulation. Results are discussed in relation to studies on human-dog communication, attachment, mood modification and joint attention.

  6. Dogs' social referencing towards owners and strangers.

    Science.gov (United States)

    Merola, Isabella; Prato-Previde, Emanuela; Marshall-Pescini, Sarah

    2012-01-01

    Social referencing is a process whereby an individual uses the emotional information provided by an informant about a novel object/stimulus to guide his/her own future behaviour towards it. In this study adult dogs were tested in a social referencing paradigm involving a potentially scary object with either their owner or a stranger acting as the informant and delivering either a positive or negative emotional message. The aim was to evaluate the influence of the informant's identity on the dogs' referential looking behaviour and behavioural regulation when the message was delivered using only vocal and facial emotional expressions. Results show that most dogs looked referentially at the informant, regardless of his/her identity. Furthermore, when the owner acted as the informant dogs that received a positive emotional message changed their behaviour, looking at him/her more often and spending more time approaching the object and close to it; conversely, dogs that were given a negative message took longer to approach the object and to interact with it. Fewer differences in the dog's behaviour emerged when the informant was the stranger, suggesting that the dog-informant relationship may influence the dog's behavioural regulation. Results are discussed in relation to studies on human-dog communication, attachment, mood modification and joint attention.

  7. Social referencing in dog-owner dyads?

    Science.gov (United States)

    Merola, I; Prato-Previde, E; Marshall-Pescini, S

    2012-03-01

    Social referencing is the seeking of information from another individual to form one's own understanding and guide action. In this study, adult dogs were tested in a social referencing paradigm involving their owner and a potentially scary object. Dogs received either a positive or negative message from the owner. The aim was to evaluate the presence of referential looking to the owner, behavioural regulation based on the owner's (vocal and facial) emotional message and observational conditioning following the owner's actions towards the object. Most dogs (83%) looked referentially to the owner after looking at the strange object, thus they appear to seek information about the environment from the human, but little differences were found between dogs in the positive and negative groups as regards behavioural regulation: possible explanations for this are discussed. Finally, a strong effect of observational conditioning was found with dogs in the positive group moving closer to the fan and dogs in the negative group moving away, both mirroring their owner's behaviour. Results are discussed in relation to studies on human-dog communication, attachment and social learning.

  8. Dogs' Social Referencing towards Owners and Strangers

    Science.gov (United States)

    Merola, Isabella; Prato-Previde, Emanuela; Marshall-Pescini, Sarah

    2012-01-01

    Social referencing is a process whereby an individual uses the emotional information provided by an informant about a novel object/stimulus to guide his/her own future behaviour towards it. In this study adult dogs were tested in a social referencing paradigm involving a potentially scary object with either their owner or a stranger acting as the informant and delivering either a positive or negative emotional message. The aim was to evaluate the influence of the informant's identity on the dogs' referential looking behaviour and behavioural regulation when the message was delivered using only vocal and facial emotional expressions. Results show that most dogs looked referentially at the informant, regardless of his/her identity. Furthermore, when the owner acted as the informant dogs that received a positive emotional message changed their behaviour, looking at him/her more often and spending more time approaching the object and close to it; conversely, dogs that were given a negative message took longer to approach the object and to interact with it. Fewer differences in the dog's behaviour emerged when the informant was the stranger, suggesting that the dog-informant relationship may influence the dog's behavioural regulation. Results are discussed in relation to studies on human-dog communication, attachment, mood modification and joint attention. PMID:23071828

  9. Geomagnetic referencing in the arctic environment

    Science.gov (United States)

    Podjono, Benny; Beck, Nathan; Buchanan, Andrew; Brink, Jason; Longo, Joseph; Finn, Carol A.; Worthington, E. William

    2011-01-01

    Geomagnetic referencing is becoming an increasingly attractive alternative to north-seeking gyroscopic surveys to achieve the precise wellbore positioning essential for success in today's complex drilling programs. However, the greater magnitude of variations in the geomagnetic environment at higher latitudes makes the application of geomagnetic referencing in those areas more challenging. Precise, real-time data on those variations from relatively nearby magnetic observatories can be crucial to achieving the required accuracy, but constructing and operating an observatory in these often harsh environments poses a number of significant challenges. Operational since March 2010, the Deadhorse Magnetic Observatory (DED), located in Deadhorse, Alaska, was created through collaboration between the United States Geological Survey (USGS) and a leading oilfield services supply company. DED was designed to produce real-time geomagnetic data at the required level of accuracy, and to do so reliably under the extreme temperatures and harsh weather conditions often experienced in the area. The observatory will serve a number of key scientific communities as well as the oilfield drilling industry, and has already played a vital role in the success of several commercial ventures in the area, providing essential, accurate data while offering significant cost and time savings, compared with traditional surveying techniques.

  10. Genomes

    National Research Council Canada - National Science Library

    Brown, T. A. (Terence A.)

    2002-01-01

    ... of genome expression and replication processes, and transcriptomics and proteomics. This text is richly illustrated with clear, easy-to-follow, full color diagrams, which are downloadable from the book's website...

  11. A general pipeline for the development of anchor markers for comparative genomics in plants

    Directory of Open Access Journals (Sweden)

    Stougaard Jens

    2006-08-01

    Full Text Available Abstract Background Complete or near-complete genomic sequence information is presently only available for a few plant species representing a large phylogenetic diversity among plants. In order to effectively transfer this information to species lacking sequence information, comparative genomic tools need to be developed. Molecular markers permitting cross-species mapping along co-linear genomic regions are central to comparative genomics. These "anchor" markers, defining unique loci in genetic linkage maps of multiple species, are gene-based and possess a number of features that make them relatively sparse. To identify potential anchor marker sequences more efficiently, we have established an automated bioinformatic pipeline that combines multi-species Expressed Sequence Tags (EST and genome sequence data. Results Taking advantage of sequence data from related species, the pipeline identifies evolutionarily conserved sequences that are likely to define unique orthologous loci in most species of the same phylogenetic clade. The key features are the identification of evolutionarily conserved sequences followed by automated design of intron-flanking Polymerase Chain Reaction (PCR primer pairs. Polymorphisms can subsequently be identified by size- or sequence variation of PCR products, amplified from mapping parents or populations. We illustrate our procedure in legumes and grasses and exemplify its application in legumes, where model plant studies and the genome- and EST-sequence data available have a potential impact on the breeding of crop species and on our understanding of the evolution of this large and diverse family. Conclusion We provide a database of 459 candidate anchor loci which have the potential to serve as map anchors in more than 18,000 legume species, a number of which are of agricultural importance. For grasses, the database contains 1335 candidate anchor loci. Based on this database, we have evaluated 76 candidate anchor loci

  12. Self-referencing Taper Curves for Loblolly Pine

    Science.gov (United States)

    Mike Strub; Chris Cieszewski; David Hyink

    2005-01-01

    We compare the traditional fitting of relative diameter over relative height with methods based on self-referencing functions and stochastic parameter estimation using data collected by the Virginia Polytechnic Institute and State University Growth and Yield Cooperative. Two sets of self-referencing equations assume known diameter at 4.5 feet inside (dib) and outside (...

  13. VT Linear Referencing System - Town-Based 2013

    Data.gov (United States)

    Vermont Center for Geographic Information — LRS2013 is a Linear Referencing System layer that includes Interstate, U.S., State (VT), and other transportation routes logged by the Vermont Agency of...

  14. Referencing Tool for Reputation and Trust in Wireless Sensor Networks

    OpenAIRE

    Salam, Mohammad Abdus; Sarkodee-Adoo, Alfred

    2015-01-01

    Presently, there are not many literatures on the characterization of reputation and trust in wireless sensor networks (WSNs) which can be referenced by scientists, researchers and students. Although some research documents include information on reputation and trust, characterization of these features are not adequately covered. In this paper, reputation and trust are divided into various classes or categories and a method of referencing the information is provided. This method used results i...

  15. Empowering Student Learning Through Rubric-Referenced Self-Assessment*

    Science.gov (United States)

    He, Xiaohua; Canty, Anne

    2012-01-01

    Purpose: The purpose of this study was to investigate the effect of rubric-referenced self-assessment on performance of anatomy assignments in a group of chiropractic students. Methods: Participants (N = 259) were first-quarter students who were divided into a treatment group (n = 130) and a comparison group (n = 129). The intervention for both groups involved the use of rubrics to complete the first draft of assignments. General feedback was given by the instructor, and then the students had the opportunity to amend the assignments before resubmission (second draft). The treatment group, however, was also asked to perform rubric-referenced self-assessment of their assignments during their second draft. Although the comparison group was also provided with the identical rubrics for the assignments, the students in this group did not perform rubric-referenced self-assessment. Results: The results revealed that the students in the treatment group who used a rubric-referenced self-assessment learning tool received statistically significant higher scores than the comparison group, who did not use this rubric-referenced self-assessment tool. Conclusion: This study suggests that practicing rubric-referenced self-assessment enhances student performance on assignments. However, educators continue to face the challenge of developing practical and useful rubric tools for student self-assessment PMID:22778527

  16. The Assessment of Critical Thinking Skill for Early Age Children Based on Criterion Referenced and Norm Referenced Interpretations

    Directory of Open Access Journals (Sweden)

    Rodhoty Taza Mila

    2016-11-01

    Full Text Available Abstract The objective of this research is to study comprehensively the assessment of critical thinking skill for early age children based on criterion referenced and norm referenced interpretations. It is a non-experimental quantitative research for students in Assalam Kinder-garten. There are some critical thinking skill indicators, such as clarity, accuracy, precision, depth, breath, relevance, and logic. By using assessment based on criterion referenced inter-pretations, critical thinking skill  is so real and absolute, while by using assessment based on norm referenced interpretations, critical thinking skill is so relative depends on their groups. Based on criterion referenced interpretations, there are 24 students can’t think critically because their scores are lower than minimum limit and 10 students can think critically because their scores are higher than minimum limit. Based on norm referenced interpreta-tions, there are 19 students think critically above average and 15 students think critically under average. So, the assessment of critical thinking skill for early age children can be strong foundation to prepare the best stimulation for optimalizing their critical thinking skill until mature in the future. Abstrak Tujuan dari penelitian ini adalah untuk mempelajari secara komprehensif penilaian keterampilan berpikir kritis untuk anak-anak usia dini berdasarkan penilaian acuan kriteria dan penilaian acuan norma. Ini merupakan penelitian kuantitatif non-eksperimental untuk siswa di TK Assalam. Ada beberapa indikator keterampilan berpikir kritis, seperti kejelasan, akurasi, presisi, kedalaman, keluasan, relevansi, dan logika. Dengan menggunakan penilaian acuan kriteria, keterampilan berpikir kritis menjadi nyata dan mutlak, sementara dengan menggunakan penilaian acuan norma, keterampilan berpikir kritis menjadi sangat relatif tergantung pada kelompok mereka. Berdasarkan penilaian acuan kriteria, ada 24 siswa tidak dapat berpikir

  17. Student Responses to Criteria-Referenced Self-Assessment

    Science.gov (United States)

    Andrade, Heidi; Du, Ying

    2007-01-01

    This paper reports on a study of undergraduate students' experiences with criteria-referenced self-assessment. Fourteen students who had taken a course involving self-assessment were interviewed in focus groups segregated by gender. The findings suggest that students had positive attitudes toward self-assessment after extended practice; felt they…

  18. Anaphoric Referencing: A Cohesive Device in Written and Spoken ...

    African Journals Online (AJOL)

    ... \\'hang together\\' to convey meaning. This study sought to find out what these devices are and paid attention to anaphoric references as a cohesive device. It looked into what differentiated anaphora from deictic expressions and the different language mechanisms for anaphoric referencing. African Research Review Vol.

  19. A Criterion-Referenced Approach to Student Ratings of Instruction

    Science.gov (United States)

    Meyer, J. Patrick; Doromal, Justin B.; Wei, Xiaoxin; Zhu, Shi

    2017-01-01

    We developed a criterion-referenced student rating of instruction (SRI) to facilitate formative assessment of teaching. It involves four dimensions of teaching quality that are grounded in current instructional design principles: Organization and structure, Assessment and feedback, Personal interactions, and Academic rigor. Using item response…

  20. 76 FR 75840 - Revising Standards Referenced in the Acetylene Standard

    Science.gov (United States)

    2011-12-05

    .... OSHA-2011-0183] RIN 1218-AC64 Revising Standards Referenced in the Acetylene Standard AGENCY: Occupational Safety and Health Administration (OSHA), Department of Labor. ACTION: Notice of proposed... standards developing organization (``SDO standards''). OSHA also is publishing a direct final rule in today...

  1. Postgraduate nursing student knowledge, attitudes, skills, and confidence in appropriately referencing academic work.

    Science.gov (United States)

    Greenwood, Melanie; Walkem, Kerrie; Smith, Lindsay Mervyn; Shearer, Toniele; Stirling, Christine

    2014-08-01

    Preventing plagiarism is an ongoing issue for higher education institutions. Although plagiarism has been traditionally seen as cheating, it is increasingly thought to be the result of poor referencing, with students reporting difficulties citing and referencing bibliographic sources. This study examined the academic knowledge, attitude, skills, and confidence of students in a school of nursing to understand poor referencing. A cross-sectional quantitative and qualitative survey was distributed to postgraduate (N = 1,000) certificate, diploma, and master's students. Quantitative data gathered demographics, cultural and linguistic background, and use of technology. Thematic analysis discovered patterns and themes. Results showed participants understood requirements for referencing; half indicated poor referencing was due to difficulty referencing Internet sources or losing track of sources, and many lacked confidence in key referencing tasks. Despite this, 50% did not make use of referencing resources. Overall, these data suggest incorrect referencing is rarely intentional and predominantly caused by skills deficit. Copyright 2014, SLACK Incorporated.

  2. Energy Referencing in LANL HE-EOS Codes

    Energy Technology Data Exchange (ETDEWEB)

    Leiding, Jeffery Allen [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Coe, Joshua Damon [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2017-10-19

    Here, We briefly describe the choice of energy referencing in LANL's HE-EOS codes, HEOS and MAGPIE. Understanding this is essential to comparing energies produced by different EOS codes, as well as to the correct calculation of shock Hugoniots of HEs and other materials. In all equations after (3) throughout this report, all energies, enthalpies and volumes are assumed to be molar quantities.

  3. Time domain referencing in intensity modulation fiber optic sensing systems

    Science.gov (United States)

    Adamovsky, G.

    1986-01-01

    Intensity modulation sensors are classified depending on the way in which the reference and signal channels are separated: in space, wavelength (frequency), or time domains. To implement the time domain referencing different types of fiber optic (FO) loops have been used. A pulse of short duration sent into the loop results in a series of pulses of different amplitudes. The information about the measured parameter is retrieved from the relative amplitudes of pulses in the same train.

  4. Four activities to promote student engagement with referencing skills

    OpenAIRE

    Williams, Gareth J.; Emerson, Anne; Larkin, Rebecca F.; Norman, Christine

    2014-01-01

    Teaching academic writing skills in a way that engages students in deep learning is difficult and there is a risk of encouraging surface learning approaches. Moreover, linking the experience of the research process to understanding the provenance of research studies is difficult for students as they tend to experience research, referencing, citing, and related areas in disparate and unconnected ways. We report our initial experiences of designing a series of four mutually supportive tutorial ...

  5. Performance Evaluation and Requirements Assessment for Gravity Gradient Referenced Navigation

    Directory of Open Access Journals (Sweden)

    Jisun Lee

    2015-07-01

    Full Text Available In this study, simulation tests for gravity gradient referenced navigation (GGRN are conducted to verify the effects of various factors such as database (DB and sensor errors, flight altitude, DB resolution, initial errors, and measurement update rates on the navigation performance. Based on the simulation results, requirements for GGRN are established for position determination with certain target accuracies. It is found that DB and sensor errors and flight altitude have strong effects on the navigation performance. In particular, a DB and sensor with accuracies of 0.1 E and 0.01 E, respectively, are required to determine the position more accurately than or at a level similar to the navigation performance of terrain referenced navigation (TRN. In most cases, the horizontal position error of GGRN is less than 100 m. However, the navigation performance of GGRN is similar to or worse than that of a pure inertial navigation system when the DB and sensor errors are 3 E or 5 E each and the flight altitude is 3000 m. Considering that the accuracy of currently available gradiometers is about 3 E or 5 E, GGRN does not show much advantage over TRN at present. However, GGRN is expected to exhibit much better performance in the near future when accurate DBs and gravity gradiometer are available.

  6. PC-based visualization of geographically referenced environmental data

    International Nuclear Information System (INIS)

    Galagan, C.; Howlett, E. Brown, A.J.

    1992-01-01

    Geographical information system (GIS) technology provides sophisticated data handling tools for use in oil spill response and contingency planning. ASAMAP is a software that employs a state-of-the-art graphical user interface to collect and display geographically referenced data on a personal computer. The program is easy to learn and simple to operate, facilitating data collection and visualization in an inexpensive decision support system suitable for oil spill response or any application requiring special data handling. The software can operate on a laptop computer for convenient use in the field and is mouse-driven, using buttons and screen icons to manipulate data interactively on color maps on the screen. During response to an oil spill, ASAMAP provides enhanced data capture and visualization, facilitating faster assimilation of information and a more efficient decision making process. 8 refs., 1 fig

  7. Unemployment estimation: Spatial point referenced methods and models

    KAUST Repository

    Pereira, Soraia

    2017-06-26

    Portuguese Labor force survey, from 4th quarter of 2014 onwards, started geo-referencing the sampling units, namely the dwellings in which the surveys are carried. This opens new possibilities in analysing and estimating unemployment and its spatial distribution across any region. The labor force survey choose, according to an preestablished sampling criteria, a certain number of dwellings across the nation and survey the number of unemployed in these dwellings. Based on this survey, the National Statistical Institute of Portugal presently uses direct estimation methods to estimate the national unemployment figures. Recently, there has been increased interest in estimating these figures in smaller areas. Direct estimation methods, due to reduced sampling sizes in small areas, tend to produce fairly large sampling variations therefore model based methods, which tend to

  8. Orthogonally referenced integrated ensemble for navigation and timing

    Science.gov (United States)

    Smith, Stephen Fulton; Moore, James Anthony

    2014-04-01

    An orthogonally referenced integrated ensemble for navigation and timing includes a dual-polyhedral oscillator array, including an outer sensing array of oscillators and an inner clock array of oscillators situated inside the outer sensing array. The outer sensing array includes a first pair of sensing oscillators situated along a first axis of the outer sensing array, a second pair of sensing oscillators situated along a second axis of the outer sensing array, and a third pair of sensing oscillators situated along a third axis of the outer sensing array. The inner clock array of oscillators includes a first pair of clock oscillators situated along a first axis of the inner clock array, a second pair of clock oscillators situated along a second axis of the inner clock array, and a third pair of clock oscillators situated along a third axis of the inner clock array.

  9. The posterior condylar offset ratio and femoral anatomy in anterior versus posterior referencing total knee arthroplasty.

    Science.gov (United States)

    Almeida, P H; Vilaça, A

    2015-10-01

    The preservation of joint anatomy is one of the key issues in total knee arthroplasty. The effect of the prosthesis' referencing system, relative to femoral anatomy, remains unknown. It was sought to determine if femoral anatomy, following total knee arthroplasty is better maintained using either anterior referencing or posterior referencing prosthesis. The posterior condylar offset ratio (PCOR) was employed for preoperative and postoperative radiographic comparison of femoral condyles. It was hypothesized that posterior referencing prosthesis would better restore condylar morphology. Sixty-six patients undergoing a total knee arthroplasty with anterior referenced Zimmer(®) NexGen(®) LPS prosthesis and ninety-one with posterior referenced Tornier(®) HLS Noetos(®) were divided into two groups according to the prosthetic model used and retrospectively compared. PCOR was calculated as the quotient of the distance between the posterior condylar border and the tangent to the posterior cortex of the femoral diaphysis, and the distance between the posterior condylar border and the tangent to the anterior cortex of the femoral diaphysis. PCOR was determined preoperatively and postoperatively and compared within each group and between both groups. An increase in the PCOR (Panterior referencing and posterior referencing models. No difference was noted when the postoperative PCOR was compared between both groups (P=0.61). Both anterior and posterior referencing prosthesis lead to a similar increase of the PCOR following total knee arthroplasty. Level IV. Copyright © 2015 Elsevier Masson SAS. All rights reserved.

  10. Criteria referenced student self-assesment in restorative dentistry.

    Science.gov (United States)

    Bookhan, V; Becker, L H; Oosthuizen, M P

    2005-05-01

    The application of criteria referenced assessment has been previously reported, however, criteria referenced self-assessment has not yet been studied. The objective of this study was to develop and use clear and explicit criteria, linked to a level of competency and a score, as well as a checklist, for student self-assessment in Restorative Dentistry. A comparison of student self-assessment and supervisor-assessment was also undertaken to determine the validity and reliability of the criteria. Six levels of competency were adapted from the literature and a criterion was developed for each level of competency and used for student self-assessment of clinical procedures in Restorative Dentistry (BChD IV and BChD V). Each level of competency was given a score: U = Unqualified (0), NBQ = Not becoming Qualified (1), BQB = Becoming Qualified as a Beginner (2), BQL = Becoming Qualified as a Learner (3), Q = Qualified (4), E = Exceptional (5). The students used the criteria on the assessment form, to assess themselves accordingly (U, NBQ, BQB, BQL, Q, E) and this was compared to the supervisor assessment using the same criteria. The results were subjected to a Spearman Rank-Order Correlation test. The Spearman Correlation Coefficient for the BChD V group was 0.882 and 0.927 for the BChD IV group in the first semester and 0.923 for the BChD V group and 0.900 for the BChD IV group in the second semester. The results were highly significant (pDentistry is valid and reliable.

  11. Characteristics of Criterion-Referenced Instruments: Implications for Materials Selection for the Learning Disabled.

    Science.gov (United States)

    Blasi, Joyce F.

    Discussed are characteristics of criterion referenced reading tests for use with learning disabled (LD) children, and analyzed are the Basic Educational Skills Inventory (BESI), the Prescriptive Reading Inventory (PRI), and the Cooper-McGuire Diagnostic Work-Analysis Test (CooperMcGuire). Criterion referenced tests are defined; and problems in…

  12. Validity and Reliability of Criterion-Referenced Measures: Issues and Procedures for Special Educators.

    Science.gov (United States)

    Harris, Larry P.; Wolf, Steven R.

    1979-01-01

    The article focuses on the controversy over norm-referenced v criterion-referenced measures (CRM) in assessment of learning disorders. The authors contend that while the reliability of CRMs is generally indisputable, the validity of measures designed from local curricula is still dependent on the intuitive judgments of teachers. (Author/SBH)

  13. Energy Conversion: A Comparison of Fix- and Self-Referenced Wave Energy Converters

    Directory of Open Access Journals (Sweden)

    Wanan Sheng

    2016-12-01

    Full Text Available The paper presents an investigation of fix-referenced and self-referenced wave energy converters and a comparison of their corresponding wave energy conversion capacities from real seas. For conducting the comparisons, two popular wave energy converters, point absorber and oscillating water column, and their power conversion capacities in the fixed-referenced and self-referenced forms have been numerically studied and compared. In the numerical models, the device’s power extractions from seas are maximized using the correspondingly optimized power take-offs in different sea states, thus their power conversion capacities can be calculated and compared. From the comparisons and analyses, it is shown that the energy conversion capacities of the self-referenced devices can be significantly increased if the motions of the device itself can be utilized for wave energy conversion; and the self-referenced devices can be possibly designed to be compliant in long waves, which could be a very beneficial factor for device survivability in the extreme wave conditions (normally long waves. In this regards, the self-referenced WECs (wave energy converters may be better options in terms of wave energy conversion from the targeted waves in seas (frequently the most occurred, and in terms of the device survivability, especially in the extreme waves when compared to the fix-referenced counterparts.

  14. Six Single-Administration Reliability Coefficients for Criterion-Referenced Tests: A Comparative Study.

    Science.gov (United States)

    Downing, Steven M.; Mehrens, William A.

    Four criterion-referenced reliability coefficicents were compared to the Kuder-Richardson estimates and to each other. The Kuder-Richardson formulas 20 and 21, the Livingston, the Subkoviak and two Huynh coefficients were computed for a random sample of 33 criterion-referenced tests. The Subkoviak coefficient yielded the highest mean value;…

  15. An Investigation Into the Use of Criterion-Referenced Measurement in Vocational and Technical Training.

    Science.gov (United States)

    Day, Gerald F.

    The paper investigates and analyses the current state of the art of criterion-referenced measurement (CRM), with a view to determining its use in training and instructional programs. It presents a reveiw of the literature pertaining to the following aspects: a brief history of CRM; a definition and comparison of criterion-referenced and…

  16. Embedding External Referencing of Standards into Higher Education: Collaborative Relationships Are the Key

    Science.gov (United States)

    Sefcik, Lesley; Bedford, Simon; Czech, Peter; Smith, Judith; Yorke, Jonathan

    2018-01-01

    External referencing of assessment and students' achievement standards is a growing priority area within higher education, which is being pressured by government requirements to evidence outcome attainment. External referencing benefits stakeholders connected to higher education by helping to assure that assessments and standards within courses…

  17. Concept-referenced spaces in Computer-supported Collaborative Work

    Science.gov (United States)

    Diviacco, Paolo; Pshenichny, Cyril

    2010-05-01

    case, to select an item from a dump, and in the latter, to decide what to put where, and why. How to balance, then, in one collaborative tool, the need to apply a fixed meaning and the claim to preserve different and concurrent meanings? Among possible paths that can be followed, we will here focus on two views that acknowledge formalism but at the same time avoid strict definitions: (I) task mapping and (II) the event bush method (Pshenichny et al., 2009). Both rely on a formalized graphic representation made of nodes (denoting abstractions or concepts) and edges, but relax on the meaning of nodes themselves, which are descriptive but not explanatory, connotative but not denotative. The former path (I) is more oriented toward human activities, e.g., a workflow of data processing. The latter (II) formalizes a domain of knowledge through relations of cause and effect as in describing geohazards. Importantly, these cause-effect relations are just postulated as observed or imagined facts, but not elucidated - e.g., "if something explodes, it falls into fragments", without an explanation. The one who denies this relation is free to build another event bush without it, and compare the structure of the two bushes to find out what else has changed with negation of this link. In both cases reasoning is projected over the graph while information (as a file resulting from an intermediate processing step, or the observations regarding the presence of water during a volcanic eruption) can be organized across the nodes of the graph. This adds to the bi-dimensional surface of the task-map or of the event bush, a third dimension creating a "concept-referenced" space (some kind of geo-referencing applied to reasoning) where collaborators can easily find the information they are looking for

  18. BioCD: Self-referencing interferometer for biosensing

    Science.gov (United States)

    Varma, Manoj

    The holy-grail of modern medical science is to provide personalized health-care. An individual's state of health can be correlated to the pattern of concentration of several 'marker' molecules, for e.g. the presence of Prostate Specific Antigen (PSA) beyond a certain threshold in the body is a strong indication of prostate cancer. To realize the dream of personalized healthcare, a large number of markers have to be identified and correlated to the state of health across diverse populations. The identified markers have to be quantified subsequently to define an individual's state of health. The technology used to achieve the above should be sensitive, accurate, reliable, high-throughput and should be cheap and simple enough to be able to be available in a clinician's office. Interferometry has been used as a sensitive metrology tool in fields ranging from semiconductor inspection to astronomy. This thesis demonstrates a self-referencing interferometric biosensor (BioCD) with a surface normal design potentially capable of scaling up to thousands of tests per sensor substrates. The sensor concept is similar to an optical CD in that gold microstructures fabricated on the BioCD surface act as wavefront splitting interferometers. In contrast to the optical CD, the BioCD operates in a condition called quadrature, which provides maximum linear response to small phase changes caused by protein binding events. The gold microstructures generate a carrier wave when the BioCD is spun, and protein binding is detected as a modulation of an envelope of the carrier wave pattern created by the immobilized capture proteins. By immobilizing reference and target proteins, differential measurements that automatically subtract out non-specific binding can be obtained. We have demonstrated a detection limit of about 1 ng/ml with this technology, which is a clinically relevant figure for many human and veterinary applications. The specific and non-specific binding signals are separated by

  19. Near Real-Time Dissemination of Geo-Referenced Imagery by an Enterprise Server

    National Research Council Canada - National Science Library

    Brown, Alison; Gilbert, Chris; Holland, Heather; Lu, Yan

    2006-01-01

    .... The payload is connected through a data link to a ground-based server that can process the georegistered data in near-real-time using our GeoReferenced Information Manager (GRIM) Enterprise Server...

  20. Ten Issues in Criterion-Referenced Testing: A Response to Commonly Heard Criticisms.

    Science.gov (United States)

    Curlette, William L.; Stallings, William M.

    1979-01-01

    The 10 criticisms of criterion-referenced tests addressed in this paper are: the domains tested; pedagogical influence; difficulty of items; cumbersome reports; reliability; arbitrary criteria; local objectives; labeling; predictive validity; and repeated testing. (SJL)

  1. A new compact self-referenced holographic setup tested on a fluorescent target

    OpenAIRE

    Kiss, Márton Zsolt

    2015-01-01

    We propose a new self-referenced holographic microscope setup based on a special bifocal lens. This setup can detect and visualize fluorescent objects. The new principle and the experimental results of the imaging are also presented.

  2. Helping me, helping you: self-referencing and gender roles in donor advertising.

    Science.gov (United States)

    Hupfer, M E

    2006-06-01

    Donor advertising typically emphasizes altruism, but an appeal to individual self-interest may be more effective in heightening blood donation intentions among youthful nondonors. A total of 292 undergraduate business students at a Canadian university provided complete data in response to a between-subjects full-factorial advertising experiment with sex, self-referencing, and message strategy factors. Self-referencing, or mental processing that links information to the self-concept, was elicited at either a low or moderate level, whereas the message strategy was either agentic (donate blood because you may need it yourself) or communal (donate blood because someone close to you may need it). Dependent variables included identification with the ad, donation intentions, and a discrimination measure of recognition memory. A three-way interaction among sex, self-referencing level (low or moderate), and message (agentic or communal) was found. Two-way self-referencing by message graphs of donation intentions and ad identification showed a parallel structure for males in that their responses were generally more favorable when self-referencing was at a moderate level, regardless of the message type. Among women, however, crossover interactions between the level of self-referencing and the message type (agentic vs. communal) were observed, such that the message's effect differed with the level of self-referencing. For both men and women, the agentic message was more effective than communal ad copy when a moderate level of self-referencing was achieved. Collection agencies should consider appealing to young nondonors by suggesting that they give blood to make it available for themselves if required.

  3. R@P: developing and promoting the Referencing@Portsmouth service

    OpenAIRE

    Matthews, J.; Gwyer, Roisin; Jones, Linda; Worden, Anne

    2009-01-01

    The library at the University of Portsmouth (UoP) has for some years been providing advice on referencing across the institution, either at enquiry desks or through subject/faculty librarians.In addition, annually updated short guidesto Vancouver and Harvard (American Psychological Association variant) were produced by thelibrary, and distributed to new students in their thousands. This sufficed for a time but in thelast three or four years the number of referencing enquiries being fielded by...

  4. Influence of water and fat heterogeneity on fat-referenced MR thermometry.

    Science.gov (United States)

    Baron, Paul; Deckers, Roel; Bouwman, Job G; Bakker, Chris J G; de Greef, Martijn; Viergever, Max A; Moonen, Chrit T W; Bartels, Lambertus W

    2016-03-01

    To investigate the effect of the aqueous and fatty tissue magnetic susceptibility distribution on absolute and relative temperature measurements as obtained directly from the water/fat (w/f) frequency difference. Absolute thermometry was investigated using spherical phantoms filled with pork and margarine, which were scanned in three orthogonal orientations. To evaluate relative fat referencing, multigradient echo scans were acquired before and after heating pork tissue via high-intensity focused ultrasound (HIFU). Simulations were performed to estimate the errors that can be expected in human breast tissue. The sphere experiment showed susceptibility-related errors of 8.4 °C and 0.2 °C for pork and margarine, respectively. For relative fat referencing measurements, fat showed pronounced phase changes of opposite polarity to aqueous tissue. The apparent mean temperature for a numerical breast model assumed to be 37 °C was 47.2 ± 21.6 °C. Simulations of relative fat referencing for a HIFU sonication (ΔT = 29.7 °C) yielded a maximum temperature error of 6.6 °C compared with 2.5 °C without fat referencing. Variations in the observed frequency difference between water and fat are largely due to variations in the w/f spatial distribution. This effect may lead to considerable errors in absolute MR thermometry. Additionally, fat referencing may exacerbate rather than correct for proton resonance frequency shift-temperature measurement errors. © 2015 Wiley Periodicals, Inc.

  5. Prediction errors to emotional expressions: the roles of the amygdala in social referencing.

    Science.gov (United States)

    Meffert, Harma; Brislin, Sarah J; White, Stuart F; Blair, James R

    2015-04-01

    Social referencing paradigms in humans and observational learning paradigms in animals suggest that emotional expressions are important for communicating valence. It has been proposed that these expressions initiate stimulus-reinforcement learning. Relatively little is known about the role of emotional expressions in reinforcement learning, particularly in the context of social referencing. In this study, we examined object valence learning in the context of a social referencing paradigm. Participants viewed objects and faces that turned toward the objects and displayed a fearful, happy or neutral reaction to them, while judging the gender of these faces. Notably, amygdala activation was larger when the expressions following an object were less expected. Moreover, when asked, participants were both more likely to want to approach, and showed stronger amygdala responses to, objects associated with happy relative to objects associated with fearful expressions. This suggests that the amygdala plays two roles in social referencing: (i) initiating learning regarding the valence of an object as a function of prediction errors to expressions displayed toward this object and (ii) orchestrating an emotional response to the object when value judgments are being made regarding this object. Published by Oxford University Press 2014. This work is written by US Government employees and is in the public domain in the US.

  6. Micro-capillary-based self-referencing surface plasmon resonance fiber-optic biosensor

    Science.gov (United States)

    Chen, Shimeng; Liu, Yun; Li, Lixia; Liu, Zigeng; Peng, Wei

    2016-11-01

    In this paper, we propose and demonstrate a novel self-referencing surface plasmon resonance (SPR) fiber-optic sensor which provides a Fabry-Perot (FP) interference referencing signal for temperature compensating. The sensor is fabricated by splicing a capillary partly coated with gold film between multimode fibers. The multimode fibers act as the lead-in and lead-out fibers while the capillary is used as sensing element. Because the FP interference and SPR effects can occur in the capillary simultaneously, the spectrum of the sensor exhibits SPR absorption and FP interference fringes. Due to the FP interference fringe sensitive to temperature while insensitive to refractive index (RI), it can be used as referencing signal and the SPR absorption was used as measuring signal. Experimental results show that this approach we presented can compensate temperature effect and develop this sensor as a practicable high-sensitivity sensing device. Moreover, as a self-referencing fiber-optic SPR sensor, this simple and low-cost element can be used for highly sensitive biosensing for further investigations.

  7. The Development of Discourse Referencing in Cantonese of Deaf/Hard-of-Hearing Children

    Science.gov (United States)

    Sze, Felix; Tang, Gladys; Lau, Tammy; Lam, Emily; Yiu, Chris

    2015-01-01

    This paper investigates the development of discourse referencing in spoken Cantonese of fifteen deaf/hard-of-hearing children studying in a sign bilingual and co-enrolment education programme in a mainstream setting in Hong Kong. A comparison of their elicited narratives with those of the hearing children and adults shows that, despite a delay in…

  8. A Psychometric Review of Norm-Referenced Tests Used to Assess Phonological Error Patterns

    Science.gov (United States)

    Kirk, Celia; Vigeland, Laura

    2014-01-01

    Purpose: The authors provide a review of the psychometric properties of 6 norm-referenced tests designed to measure children's phonological error patterns. Three aspects of the tests' psychometric adequacy were evaluated: the normative sample, reliability, and validity. Method: The specific criteria used for determining the psychometric…

  9. Adaptions of ArcGIS' Linear Referencing System to the Coastal Environment

    DEFF Research Database (Denmark)

    Balstrøm, Thomas

    2008-01-01

    For many years it has been problematic to store information for the coastal environment in a GIS. However, a system named "Linear referencing System" based upon a dynamic segmentation principle implemented in ESRIs ArcGIS 9 software has now made it possible to store and analyze information...

  10. Real-time geo-referenced video mosaicking with the MATISSE system

    DEFF Research Database (Denmark)

    Vincent, Anne-Gaelle; Pessel, Nathalie; Borgetto, Manon

    This paper presents the MATISSE system: Mosaicking Advanced Technologies Integrated in a Single Software Environment. This system aims at producing in-line and off-line geo-referenced video mosaics of seabed given a video input and navigation data. It is based upon several techniques of image...

  11. Referencing Patterns in C&RL and JAL, 1984-1986: A Bibliometric Analysis.

    Science.gov (United States)

    Lockett, Mary W.; Khawam, Yves J.

    1990-01-01

    Reports results of a bibliometric analysis of referencing patterns within journal articles published in "College and Research Libraries" (C&RL) and the "Journal of Academic Librarianship" (JAL) from 1984 through 1986. Comparisons are made between scholarliness, commonality of research bases, and relative contributions; and…

  12. Web 2.0 Authorship: Issues of Referencing and Citation for Academic Integrity

    Science.gov (United States)

    Gray, Kathleen; Thompson, Celia; Clerehan, Rosemary; Sheard, Judithe; Hamilton, Margaret

    2008-01-01

    Web 2.0 authoring forms such as wikis and blogs, social bookmarking, and audio and video podcasting pose a challenge to academic authorship traditions. This paper reviews the provisions made in major academic referencing and citation style guides for acknowledging content and ideas that may be published using these new web authoring forms. It…

  13. Agreement Coefficients as Indices of Dependability for Domain-Referenced Tests. ACT Technical Bulletin No. 28.

    Science.gov (United States)

    Kane, Michael T.; Brennan, Robert L.

    A large number of seemingly diverse coefficients have been proposed as indices of dependability, or reliability, for domain-referenced and/or mastery tests. In this paper, it is shown that most of these indices are special cases of two generalized indices of agreement: one that is corrected for chance, and one that is not. The special cases of…

  14. Teaching conceptually referenced core vocabulary for initial augmentative and alternative communication.

    Science.gov (United States)

    Snodgrass, Melinda R; Stoner, Julia B; Angell, Maureen E

    2013-12-01

    Individuals with significant intellectual disabilities who use augmentative and alternative communication (AAC) often fail to acquire large vocabularies. To maximize the functionality of a small vocabulary, AAC users' initial vocabulary typically consists of words that can be used frequently across contexts and functions (i.e., core vocabulary). For many AAC users, core vocabulary often references concepts rather than concrete items. For individuals with severe intellectual disabilities, however, initial AAC vocabulary often consists of concretely referenced words instead. There is little evidence that these individuals can learn to use conceptually referenced words in initial AAC. A variation of a single subject multiple baseline design across four stimuli was used to demonstrate that an individual with severe intellectual disabilities could learn to use conceptually referenced words as an initial AAC vocabulary. As a result of the intervention (a modified PECS procedure), a 9-year-old boy with multiple disabilities, including intellectual disability and deaf-blindness, learned to make appropriate use of three conceptually referenced tactile symbols for the concepts of more, done, and new as an initial communication vocabulary.

  15. Our teacher likes you, so I like you : A social network approach to social referencing

    NARCIS (Netherlands)

    Hendrickx, Marloes M.H.G.; Mainhard, Tim; Boor-Klip, Henrike J.; Brekelmans, Mieke

    2017-01-01

    A teacher is a social referent for peer liking and disliking when students adjust their evaluations of a peer based on their perceptions of teacher liking and disliking for this peer. The present study investigated social referencing as an intra-individual process that occurs over time, using

  16. Criterion-Referenced Test (CRT) Items for Air Conditioning, Heating and Refrigeration.

    Science.gov (United States)

    Davis, Diane, Ed.

    These criterion-referenced test (CRT) items for air conditioning, heating, and refrigeration are keyed to the Missouri Air Conditioning, Heating, and Refrigeration Competency Profile. The items are designed to work with both the Vocational Instructional Management System and Vocational Administrative Management System. For word processing and…

  17. Me, myself, and Ikea : Qualifying generic self-referencing effects in brand judgment

    NARCIS (Netherlands)

    Fennis, Bob M.; Wiebenga, Jacob H.

    The present research extends previous work on the latent tendency to be attracted to objects, events and entities that are associated with the self by demonstrating when and how generic self-referencing brand names influence brand judgment. In five studies we hypothesize and find that using pronouns

  18. Integrated GNSS attitude determination and positioning for direct geo-referencing

    NARCIS (Netherlands)

    Nadarajah, N.; Paffenholz, J.A.; Teunissen, P.J.G.

    2014-01-01

    Direct geo-referencing is an efficient methodology for the fast acquisition of 3D spatial data. It requires the fusion of spatial data acquisition sensors with navigation sensors, such as Global Navigation Satellite System (GNSS) receivers. In this contribution, we consider an integrated GNSS

  19. Student Assessment System. Domain Referenced Tests. Transportation/Automotive Mechanics. Volume II: Theory. Georgia Vocational Education Program Articulation.

    Science.gov (United States)

    Watkins, James F., Comp.

    These written domain referenced tests (DRTs) for the area of transportation/automotive mechanics test cognitive abilities or knowledge of theory. Introductory materials describe domain referenced testing and test development. Each multiple choice test includes a domain statement, describing the behavior and content of the domain, and a test item…

  20. Genomic Testing

    Science.gov (United States)

    ... Events and Multimedia Implementation Genetics 101 Family Health History Genomics and Diseases Genetic Counseling Genomic Testing Epidemiology Pathogen Genomics Resources Genomic Testing Recommend on Facebook Tweet Share Compartir Fact Sheet: Identifying Opportunities to ...

  1. Self-referenced directional enhanced Raman scattering using plasmon waveguide resonance for surface and bulk sensing

    Science.gov (United States)

    Wan, Xiu-mei; Gao, Ran; Lu, Dan-feng; Qi, Zhi-mei

    2018-01-01

    Surface plasmon-coupled emission has been widely used in fluorescence imaging, biochemical sensing, and enhanced Raman spectroscopy. A self-referenced directional enhanced Raman scattering for simultaneous detection of surface and bulk effects by using plasmon waveguide resonance (PWR) based surface plasmon-coupled emission has been proposed and experimentally demonstrated. Raman scattering was captured on the prism side in Kretschmann-surface plasmon-coupled emission. The distinct penetration depths (δ) of the evanescent field for the transverse electric (TE) and transverse magnetic (TM) modes result in different detected distances of the Raman signal. The experimental results demonstrate that the self-referenced directional enhanced Raman scattering of the TE and TM modes based on the PWR can detect and distinguish the surface and bulk effects simultaneously, which appears to have potential applications in researches of chemistry, medicine, and biology.

  2. Self-referenced memory, social cognition, and symptom presentation in autism.

    Science.gov (United States)

    Henderson, Heather A; Zahka, Nicole E; Kojkowski, Nicole M; Inge, Anne P; Schwartz, Caley B; Hileman, Camilla M; Coman, Drew C; Mundy, Peter C

    2009-07-01

    We examined performance on a self-referenced memory (SRM) task for higher-functioning children with autism (HFA) and a matched comparison group. SRM performance was examined in relation to symptom severity and social cognitive tests of mentalizing. Sixty-two children (31 HFA, 31 comparison; 8-16 years) completed a SRM task in which they read a list of words and decided whether the word described something about them, something about Harry Potter, or contained a certain number of letters. They then identified words that were familiar from a longer list. Dependent measures were memory performance (d') in each of the three encoding conditions as well as a self-memory bias score (d' self-d' other). Children completed The Strange Stories Task and The Children's Eyes Test as measures of social cognition. Parents completed the SCQ and ASSQ as measures of symptom severity. Children in the comparison sample showed the standard SRM effect in which they recognized significantly more self-referenced words relative to words in the other-referenced and letter conditions. In contrast, HFA children showed comparable rates of recognition for self- and other-referenced words. For all children, SRM performance improved with age and enhanced SRM performance was related to lower levels of social problems. These associations were not accounted for by performance on the mentalizing tasks. Children with HFA did not show the standard enhanced processing of self- vs. other-relevant information. Individual differences in the tendency to preferentially process self-relevant information may be associated with social cognitive processes that serve to modify the expression of social symptoms in children with autism.

  3. Real-time geo-referenced video mosaicking with the MATISSE system

    DEFF Research Database (Denmark)

    Vincent, Anne-Gaelle; Pessel, Nathalie; Borgetto, Manon

    This paper presents the MATISSE system: Mosaicking Advanced Technologies Integrated in a Single Software Environment. This system aims at producing in-line and off-line geo-referenced video mosaics of seabed given a video input and navigation data. It is based upon several techniques of image and...... and signal processing which have been developed at Ifremer these last years in the fields of image mosaicking, camera self-calibration or correction and estimation of navigation data....

  4. A statistically robust EEG re-referencing procedure to mitigate reference effect

    OpenAIRE

    Lepage, Kyle Q.; Kramer, Mark A.; Chu, Catherine J.

    2014-01-01

    Background: The electroencephalogram (EEG) remains the primary tool for diagnosis of abnormal brain activity in clinical neurology and for in vivo recordings of human neurophysiology in neuroscience research. In EEG data acquisition, voltage is measured at positions on the scalp with respect to a reference electrode. When this reference electrode responds to electrical activity or artifact all electrodes are affected. Successful analysis of EEG data often involves re-referencing procedures th...

  5. AIDE Project: Deliverable D5.1 (Software Library for indoor location) and referenced documents

    OpenAIRE

    Amat, Guillermo

    2017-01-01

    This publication includes the Deliverable 5.1 (Software Library for indoor location) of the AIDE Project (G.A.645322) and the following documents that are referenced in the deliverable: [1] Zed AIDE Research & Development Team (2016). Indoor Mapping Guide. [2] Zed AIDE Research & Development Team (2016). AIDE Location Services. [3] Zed AIDE Research & Development Team (2016). AIDE YARP Wrapper for Location Services. [4] Zed AIDE Research & Development Team (2016). AIDE Contextual...

  6. Rate of self-referencing int he journal Radiologia: An indicator of quality

    International Nuclear Information System (INIS)

    Miguel, A.; Marti-Bonmati, L.

    2000-01-01

    Self-referencing, defined as the number of times articles published in a scientific journal cite previous articles printed in the same journal, is an important indicator of quality. Our purpose was to analyze the rate of self-referencing in the journal Radiologia. All the articles published in Radiologia from 1994 to 1998 were analyzed to determine the index of references to Radiologia (IRR) and the index of articles that refer to Radiologia (IAR). these indices were also calculated for European Radiology (index of references to European Radiologia (IRER) and index or articles referring to European Radiology (IAER), a journal that is listed in the Index Medicus, for the year 1998. Between 1994 and 1998, the IRR ranged from 1.5% to 1,9%. In 1998, it was 1.8% while the IRER was only 0.9%, a difference that was statistically significant (p=0.02). In that same year, the IAR was also higher than the IAER (2.3% versus 1.6%). The rate of self-referencing in Radiologia is higher than that of European Radiology, a journal that is included in the Index Medicus and its Medline database. (Author) 13 refs

  7. spBayes: An R Package for Univariate and Multivariate Hierarchical Point-referenced Spatial Models.

    Science.gov (United States)

    Finley, Andrew O; Banerjee, Sudipto; Carlin, Bradley P

    2007-04-01

    Scientists and investigators in such diverse fields as geological and environmental sciences, ecology, forestry, disease mapping, and economics often encounter spatially referenced data collected over a fixed set of locations with coordinates (latitude-longitude, Easting-Northing etc.) in a region of study. Such point-referenced or geostatistical data are often best analyzed with Bayesian hierarchical models. Unfortunately, fitting such models involves computationally intensive Markov chain Monte Carlo (MCMC) methods whose efficiency depends upon the specific problem at hand. This requires extensive coding on the part of the user and the situation is not helped by the lack of available software for such algorithms. Here, we introduce a statistical software package, spBayes, built upon the R statistical computing platform that implements a generalized template encompassing a wide variety of Gaussian spatial process models for univariate as well as multivariate point-referenced data. We discuss the algorithms behind our package and illustrate its use with a synthetic and real data example.

  8. spBayes: An R Package for Univariate and Multivariate Hierarchical Point-referenced Spatial Models

    Directory of Open Access Journals (Sweden)

    Andrew O. Finley

    2007-04-01

    Full Text Available Scientists and investigators in such diverse fields as geological and environmental sciences, ecology, forestry, disease mapping, and economics often encounter spatially referenced data collected over a fixed set of locations with coordinates (latitude–longitude, Easting–Northing etc. in a region of study. Such point-referenced or geostatistical data are often best analyzed with Bayesian hierarchical models. Unfortunately, fitting such models involves computationally intensive Markov chain Monte Carlo (MCMC methods whose efficiency depends upon the specific problem at hand. This requires extensive coding on the part of the user and the situation is not helped by the lack of available software for such algorithms. Here, we introduce a statistical software package, spBayes, built upon the R statistical computing platform that implements a generalized template encompassing a wide variety of Gaussian spatial process models for univariate as well as multivariate point-referenced data. We discuss the algorithms behind our package and illustrate its use with a synthetic and real data example.

  9. Fast accurate MR thermometry using phase referenced asymmetric spin-echo EPI at high field.

    Science.gov (United States)

    Streicher, Markus N; Schäfer, Andreas; Ivanov, Dimo; Müller, Dirk K; Amadon, Alexis; Reimer, Enrico; Huber, Laurentius; Dhital, Bibek; Rivera, Debra; Kögler, Carsten; Trampel, Robert; Pampel, André; Turner, Robert

    2014-02-01

    A novel highly accurate method for MR thermometry, effective at high field, is introduced and validated, which corrects for slow and fast field fluctuations by means of reference images. An asymmetric spin-echo echo planar imaging sequence was made frequency-selective to water or a reference substance by controlling the slice-select gradient polarity and the duration of the excitation and refocusing radiofrequency pulses. Images were acquired pairwise, and the temperature-sensitive water images were corrected for field fluctuations using the reference images. In a phantom radiofrequency heating experiment, dissolved dimethyl sulfoxide was used as a reference substance. Temperature stability was tested in vivo on the human brain, referenced using subcutaneous scalp fat. Water and fat phase images were acquired only 50 ms apart. Bloch simulations validated the frequency selection accuracy. Asymmetric spin-echo imaging using a simple frequency selection method provides highly accurate referenced MR thermometry in phantoms and in vivo at 7 T. Effects of field fluctuations caused by field drift, breathing, and heart beat were corrected. The technique is highly robust against B1 inhomogeneities. Frequency selection using gradient-reversal can enable fast accurate referenced in vivo MR thermometry, assisting thermal characterization of radiofrequency coils and possibly in vivo SAR monitoring. Copyright © 2013 Wiley Periodicals, Inc.

  10. The regulatory function of social referencing in preschoolers with Down syndrome or Williams syndrome

    Directory of Open Access Journals (Sweden)

    Thurman Angela John

    2013-02-01

    Full Text Available Abstract Background An important developmental task is to learn to recognize another person as a source of information and to utilize this information as a method of learning about the surrounding world. This socially guided form of learning, referred to as social referencing, is critical for the development of children’s understanding of other people, themselves and their surrounding world. In the present project, the regulatory function of social referencing was examined in two genetic disorders that are characterized by differing patterns of socio-cognitive development: Down syndrome (DS and Williams syndrome (WS. Methods Participants were 20 children with DS and 20 children with WS aged 42 to 71 months, matched on chronological age and gender. Each child participated in four studies: one study in which we examined performance in a social referencing paradigm and three studies in which we considered performance on tasks designed to tap each of three component abilities (initiating eye contact, gaze following and emotional responsivity important for success in social referencing. Results The majority of children in both groups demonstrated positive behavioral responses regarding the stimulus in the Social Referencing task when the adult communicated a joyful message but did not regulate their own behavior in accordance with the adult’s expression of fear. Between-group differences were observed in both conditions, with most differences indicating more advanced socio-communicative competence for children with DS than for children with WS even though the overall intellectual abilities and receptive language abilities of the children with WS were significantly higher than were those of the children with DS. The results of follow-up studies indicated that children with DS were more likely to initiate eye contact (unsolicited and to follow another person’s gaze in triadic situations than were children with WS. Neither group regulated their

  11. Real world referencing and schizophrenia: are we experiencing the same reality?

    Science.gov (United States)

    Landgraf, Steffen; Krebs, Marie-Odile; Olié, Jean-Pierre; Committeri, Giorgia; van der Meer, Elke; Berthoz, Alain; Amado, Isabelle

    2010-08-01

    Psychotic symptoms in schizophrenia patients encompass the difficulty to distinguish between the respective points of view of self and others. The capacity to adopt and switch between different perspectives is, however, fundamental for ego- and allocentric spatial referencing. We tested whether schizophrenia patients are able to adopt and maintain a non-egocentric point of view in a complex visual environment. Twenty-four chronic schizophrenic outpatients (11 females) and 25 controls matched for age, gender, years of education and handedness were recruited from a population-based sample. In a virtual environment, participants had to make a decision as to which of two trash cans was closest to themselves (viewer-centered, egocentric), to a ball (object-centered, unstable allocentric), or to a palace (landmark-centered, stable allocentric). Main outcome measures were reaction time, error rate, learning rate and local task switch cost. While egocentric reaction time was preserved, patients showed an increased reaction time in both allocentric referencing conditions (stable and unstable) and an overall increased error rate. Switch cost was diminished in patients when changing from the egocentric to the landmark-centered condition and elevated when changing from the landmark-centered to the egocentric condition. The results imply that schizophrenia patients' adoption of an egocentric perspective is preserved. However, adopting an allocentric point of view and switching between egocentric and landmark-centered perspectives are impaired. Perturbations in non-egocentric referencing and transferring efficiently between different referential systems might contribute to altered personal and social world comprehension in schizophrenia. Copyright (c) 2010 Elsevier Ltd. All rights reserved.

  12. PLUME–FEATHER, Referencing and Finding Software for Research and Education

    International Nuclear Information System (INIS)

    Hoffmann, Dirk; Romier, Geneviève

    2012-01-01

    PLUME-FEATHER is a non-profit project created to Promote economicaL, Useful and Maintained softwarE For the Higher Education And THE Research communities. The site references software, mainly Free/Libre Open Source Software (FLOSS) from French universities and national research organisations, (CNRS, INRA…), laboratories or departments as well as other FLOSS software used and evaluated by users within these institutions. Each software is represented by a reference card, which describes origin, aim, installation, cost (if applicable) and user experience from the point of view of an academic user for academic users. Presently over 1000 programs are referenced on PLUME. Although the server is maintained by a french institution, it is completely open to international contributions in the academic domainb. All contained and validated contents are visible to anonymous public, whereas registered users can contribute, starting with comments on single software reference cards up to help with the organisation and presentation of the referenced software products. This first presentation is call for (further) contributions from the HEP community.

  13. Develop Direct Geo-referencing System Based on Open Source Software and Hardware Platform

    Directory of Open Access Journals (Sweden)

    H. S. Liu

    2015-08-01

    Full Text Available Direct geo-referencing system uses the technology of remote sensing to quickly grasp images, GPS tracks, and camera position. These data allows the construction of large volumes of images with geographic coordinates. So that users can be measured directly on the images. In order to properly calculate positioning, all the sensor signals must be synchronized. Traditional aerial photography use Position and Orientation System (POS to integrate image, coordinates and camera position. However, it is very expensive. And users could not use the result immediately because the position information does not embed into image. To considerations of economy and efficiency, this study aims to develop a direct geo-referencing system based on open source software and hardware platform. After using Arduino microcontroller board to integrate the signals, we then can calculate positioning with open source software OpenCV. In the end, we use open source panorama browser, panini, and integrate all these to open source GIS software, Quantum GIS. A wholesome collection of data – a data processing system could be constructed.

  14. Develop Direct Geo-referencing System Based on Open Source Software and Hardware Platform

    Science.gov (United States)

    Liu, H. S.; Liao, H. M.

    2015-08-01

    Direct geo-referencing system uses the technology of remote sensing to quickly grasp images, GPS tracks, and camera position. These data allows the construction of large volumes of images with geographic coordinates. So that users can be measured directly on the images. In order to properly calculate positioning, all the sensor signals must be synchronized. Traditional aerial photography use Position and Orientation System (POS) to integrate image, coordinates and camera position. However, it is very expensive. And users could not use the result immediately because the position information does not embed into image. To considerations of economy and efficiency, this study aims to develop a direct geo-referencing system based on open source software and hardware platform. After using Arduino microcontroller board to integrate the signals, we then can calculate positioning with open source software OpenCV. In the end, we use open source panorama browser, panini, and integrate all these to open source GIS software, Quantum GIS. A wholesome collection of data - a data processing system could be constructed.

  15. Description of a developmental criterion-referenced assessment for promoting competence in internal medicine residents.

    Science.gov (United States)

    Varney, Andrew; Todd, Christine; Hingle, Susan; Clark, Michael

    2009-09-01

    End-of- rotation global evaluations can be subjective, produce inflated grades, lack interrater reliability, and offer information that lacks value. This article outlines the generation of a unique developmental criterion-referenced assessment that applies adult learning theory and the learner, manager, teacher model, and represents an innovative application to the American Board of Internal Medicine (ABIM) 9-point scale. We describe the process used by Southern Illinois University School of Medicine to develop rotation-specific, criterion-based evaluation anchors that evolved into an effective faculty development exercise. The intervention gave faculty a clearer understanding of the 6 Accreditation Council for Graduate Medical Education competencies, each rotation's educational goals, and how rotation design affects meaningful work-based assessment. We also describe easily attainable successes in evaluation design and pitfalls that other institutions may be able to avoid. Shifting the evaluation emphasis on the residents' development of competence has made the expectations of rotation faculty more transparent, has facilitated conversations between program director and residents, and has improved the specificity of the tool for feedback. Our findings showed the new approach reduced grade inflation compared with the ABIM end-of-rotation global evaluation form. We offer the new developmental criterion-referenced assessment as a unique application of the competences to the ABIM 9-point scale as a transferable model for improving the validity and reliability of resident evaluations across graduate medical education programs.

  16. Romanization of Referencing Styles for Arts & Humanities Science Journals in Taiwan

    Directory of Open Access Journals (Sweden)

    Chang-Huei Lin

    2016-12-01

    Full Text Available Based on Big Three referecing styles guides, namely APA, Chicago (Turabian and MLA Style, this study discusses the citation formats in which have been applied and specified for scholarly references in non-English languages, especially in Chinese language scholarly writing. This study targets on those Taiwan journals, indexed by TSSCI, THCI Core, A&HCI, SSCI and Scopus, that use the Romanization of references in Chinese journal. By analyzing their notes for contributors and the real situation of application in the Chinese cited works. In respect of the aforementioned three major referencing styles and the rules made by journals themselves, the findings are as follows: the APA, Chicago, and MLA Styles should be revised according to the practical needs of citing non-English references; academic journal publishers need to specify and provide the guidelines and templates of romanizing references in respect of contributed articles; international citation index databases providers should stipulate and provide their description style for romanizing references, and the government and major academic institutes should put more efforts to assist local scholarly journals to cope with the reference romanization problems, even at promoting a kind of consistent Pinyin principle for referencing styles for Chinese journal publishing in Taiwan.

  17. PLUME-FEATHER, referencing and finding software for research and education

    International Nuclear Information System (INIS)

    Bénassy, O; Caron, C; Ferret-Canape, C; Cheylus, A; Courcelle, E; Dantec, C; Dayre, P; Dostes, T; Durand, A; Facq, A; Gambini, G; Morris, F; Geahchan, E; Helft, C; Hoffmann, D; Ingarao, M; Joly, P; Kieffer, J; Larré, J-M; Libes, M

    2014-01-01

    PLUME-FEATHER is a non-profit project created to Promote economicaL, Useful and Maintained softwarEFor theHigher Education And THE Research communities. The site references software, mainly Free/Libre Open Source Software (FLOSS) from French universities and national research organisations, (CNRS, INRA...), laboratories or departments as well as other FLOSS software used and evaluated by users within these institutions. Each software is represented by a reference card, which describes origin, aim, installation, cost (if applicable) and user experience from the point of view of an academic user for academic users. Presently over 1000 programs are referenced on PLUME by more than 900 contributors. Although the server is maintained by a French institution, it is open to international contributions in the academic domain. All contained and validated contents are visible to anonymous public, whereas (presently more than 2000) registered users can contribute, starting with comments on single software reference cards up to help with the organisation and presentation of the referenced software products. The project has been presented to the HEP community in 2012 for the first time [1]. This is an update of the status and a call for (further) contributions.

  18. Age Differences in Self-Referencing: Evidence for Common and Distinct Encoding Strategies

    Science.gov (United States)

    Gutchess, Angela H.; Sokal, Rebecca; Coleman, Jennifer A.; Gotthilf, Gina; Grewal, Lauren; Rosa, Nicole

    2014-01-01

    Although engagement of medial prefrontal cortex (MPFC) underlies self-referencing of information for younger and older adults, the region has not consistently been implicated across age groups for the encoding of self-referenced information. We sought to determine whether making judgments about others as well as the self influenced findings in the previous study. During an fMRI session, younger and older adults encoded adjectives using only a self-reference task. For items later remembered compared to those later forgotten, both age groups robustly recruited medial prefrontal cortex, indicating common neural regions support encoding across younger and older adults when participants make only self-reference judgments. Focal age differences emerged in regions related to emotional processing and cognitive control, though these differences are more limited than in tasks in which judgments also are made about others. We conclude that making judgments about another person differently affects the ways that younger and older adults make judgments about the self, with results of a follow-up behavioral study supporting this interpretation. PMID:25223905

  19. Our teacher likes you, so I like you: A social network approach to social referencing.

    Science.gov (United States)

    Hendrickx, Marloes M H G; Mainhard, Tim; Boor-Klip, Henrike J; Brekelmans, Mieke

    2017-08-01

    A teacher is a social referent for peer liking and disliking when students adjust their evaluations of a peer based on their perceptions of teacher liking and disliking for this peer. The present study investigated social referencing as an intra-individual process that occurs over time, using stochastic actor-oriented modeling with RSiena. The co-evolution of peer-perceived teacher liking and disliking networks with peer liking and disliking networks was analyzed in 52 fifth-grade classes in the Netherlands, with 1370 students (M age =10.60). Results showed that when a student viewed the teacher to like a peer, this student would also like this peer. Regarding disliking, there was a stronger effect in the opposite direction, indicating that students' disliking a peer increased the likelihood that they would view the peer as disliked by the teacher as well. In sum, partial evidence for social referencing as an intra-individual process was found. For teachers this implies that the cues they provide regarding their liking of a student, and not necessarily their disliking, may affect individual peers' liking of this student. Copyright © 2017 Society for the Study of School Psychology. Published by Elsevier Ltd. All rights reserved.

  20. Summary: Update to ASTM guide E 1523 to charge control and charge referencing techniques in x-ray photoelectron spectroscopy

    International Nuclear Information System (INIS)

    Baer, D.R.

    2005-01-01

    An updated version of the American Society for Testing and Materials (ASTM) guide E 1523 to the methods to charge control and charge referencing techniques in x-ray photoelectron spectroscopy has been released by ASTM [Annual Book of ASTM Standards Surface Analysis (American Society for Testing and Materials, West Conshohocken, PA, 2004), Vol. 03.06]. The guide is meant to acquaint x-ray photoelectron spectroscopy (XPS) users with the various charge control and charge referencing techniques that are and have been used in the acquisition and interpretation of XPS data from surfaces of insulating specimens. The current guide has been expanded to include new references as well as recommendations for reporting information on charge control and charge referencing. The previous version of the document had been published in 1997 [D. R. Baer and K. D. Bomben, J. Vac. Sci. Technol. A 16, 754 (1998)

  1. Comparison of bottom-track to global positioning system referenced discharges measured using an acoustic Doppler current profiler

    Science.gov (United States)

    Wagner, Chad R.; Mueller, David S.

    2011-01-01

    A negative bias in discharge measurements made with an acoustic Doppler current profiler (ADCP) can be caused by the movement of sediment on or near the streambed. The integration of a global positioning system (GPS) to track the movement of the ADCP can be used to avoid the systematic negative bias associated with a moving streambed. More than 500 discharge transects from 63 discharge measurements with GPS data were collected at sites throughout the US, Canada, and New Zealand with no moving bed to compare GPS and bottom-track-referenced discharges. Although the data indicated some statistical bias depending on site conditions and type of GPS data used, these biases were typically about 0.5% or less. An assessment of differential correction sources was limited by a lack of data collected in a range of different correction sources and different GPS receivers at the same sites. Despite this limitation, the data indicate that the use of Wide Area Augmentation System (WAAS) corrected positional data is acceptable for discharge measurements using GGA as the boat-velocity reference. The discharge data based on GPS-referenced boat velocities from the VTG data string, which does not require differential correction, were comparable to the discharges based on GPS-referenced boat velocities from the differentially-corrected GGA data string. Spatial variability of measure discharges referenced to GGA, VTG and bottom-tracking is higher near the channel banks. The spatial variability of VTG-referenced discharges is correlated with the spatial distribution of maximum Horizontal Dilution of Precision (HDOP) values and the spatial variability of GGA-referenced discharges is correlated with proximity to channel banks.

  2. Self-referenced continuous-variable measurement-device-independent quantum key distribution

    Science.gov (United States)

    Wang, Yijun; Wang, Xudong; Li, Jiawei; Huang, Duan; Zhang, Ling; Guo, Ying

    2018-05-01

    We propose a scheme to remove the demand of transmitting a high-brightness local oscillator (LO) in continuous-variable measurement-device-independent quantum key distribution (CV-MDI QKD) protocol, which we call as the self-referenced (SR) CV-MDI QKD. We show that our scheme is immune to the side-channel attacks, such as the calibration attacks, the wavelength attacks and the LO fluctuation attacks, which are all exploiting the security loopholes introduced by transmitting the LO. Besides, the proposed scheme waives the necessity of complex multiplexer and demultiplexer, which can greatly simplify the QKD processes and improve the transmission efficiency. The numerical simulations under collective attacks show that all the improvements brought about by our scheme are only at the expense of slight transmission distance shortening. This scheme shows an available method to mend the security loopholes incurred by transmitting LO in CV-MDI QKD.

  3. Psychometric aspects of item mapping for criterion-referenced interpretation and bookmark standard setting.

    Science.gov (United States)

    Huynh, Huynh

    2010-01-01

    Locating an item on an achievement continuum (item mapping) is well-established in technical work for educational/psychological assessment. Applications of item mapping may be found in criterion-referenced (CR) testing (or scale anchoring, Beaton and Allen, 1992; Huynh, 1994, 1998a, 2000a, 2000b, 2006), computer-assisted testing, test form assembly, and in standard setting methods based on ordered test booklets. These methods include the bookmark standard setting originally used for the CTB/TerraNova tests (Lewis, Mitzel, Green, and Patz, 1999), the item descriptor process (Ferrara, Perie, and Johnson, 2002) and a similar process described by Wang (2003) for multiple-choice licensure and certification examinations. While item response theory (IRT) models such as the Rasch and two-parameter logistic (2PL) models traditionally place a binary item at its location, Huynh has argued in the cited papers that such mapping may not be appropriate in selecting items for CR interpretation and scale anchoring.

  4. A measured-ZMP(Zero-Moment-Point)-referenced control of biped locomotion robots

    International Nuclear Information System (INIS)

    Kume, Etsuo; Akimoto, Masayuki

    1994-01-01

    For the control of biped locomotion, the model-referenced-control or programmed control method is widely used. In this method, the instantaneous torque of actuator equipped at each joint is controlled so as to equalize measured angle to input joint angle based on the prescribed motion. The drawback is that this method can not deal with the dynamic change of walking such as that due to unknown external force. To resolve such the drawback, we propose a new control method as follows: given a prescribed motion as a set of gait, namely gait of starting walk, cyclic walk, and stopping walk including a standard trajectory of the Zero-Moment-Point (ZMP), the trunk motion to compensate the legs' motion is generated in real time using the current ZMP measured by sensing device. The proposed method will be validated through some numerical simulations. (author)

  5. Ultrafast chirped optical waveform recording using referenced heterodyning and a time microscope

    Science.gov (United States)

    Bennett, Corey Vincent

    2010-06-15

    A new technique for capturing both the amplitude and phase of an optical waveform is presented. This technique can capture signals with many THz of bandwidths in a single shot (e.g., temporal resolution of about 44 fs), or be operated repetitively at a high rate. That is, each temporal window (or frame) is captured single shot, in real time, but the process may be run repeatedly or single-shot. This invention expands upon previous work in temporal imaging by adding heterodyning, which can be self-referenced for improved precision and stability, to convert frequency chirp (the second derivative of phase with respect to time) into a time varying intensity modulation. By also including a variety of possible demultiplexing techniques, this process is scalable to recoding continuous signals.

  6. Ultrafast chirped optical waveform recorder using referenced heterodyning and a time microscope

    Science.gov (United States)

    Bennett, Corey Vincent [Livermore, CA

    2011-11-22

    A new technique for capturing both the amplitude and phase of an optical waveform is presented. This technique can capture signals with many THz of bandwidths in a single shot (e.g., temporal resolution of about 44 fs), or be operated repetitively at a high rate. That is, each temporal window (or frame) is captured single shot, in real time, but the process may be run repeatedly or single-shot. This invention expands upon previous work in temporal imaging by adding heterodyning, which can be self-referenced for improved precision and stability, to convert frequency chirp (the second derivative of phase with respect to time) into a time varying intensity modulation. By also including a variety of possible demultiplexing techniques, this process is scalable to recoding continuous signals.

  7. Mobile TDR for geo-referenced measurement of soil water content and electrical conductivity

    DEFF Research Database (Denmark)

    Thomsen, Anton; Schelde, Kirsten; Drøscher, Per

    2007-01-01

    The development of site-specific crop management is constrained by the availability of sensors for monitoring important soil and crop related conditions. A mobile time-domain reflectometry (TDR) unit for geo-referenced soil measurements has been developed and used for detailed mapping of soil water...... content and electrical conductivity within two research fields. Measurements made during the early or late season, when soil moisture levels are close to field capacity, are related to the amount of plant available water and soil texture. Combined measurements of water content and electrical conductivity...... are closely related to the clay and silt fractions of a variable field. The application to early season field mapping of water content, electrical conductivity and clay content is presented. The water and clay content maps are to be used for automated delineation of field management units. Based on a spatial...

  8. [Social networks and participation in a community referenced to a family health care unit].

    Science.gov (United States)

    Budó, Maria de Lourdes Denardin; Oliveira, Stefanie Griebeler; Garcia, Raquel Pötter; Simon, Bruna Sodré; Schimith, Maria Denise; Mattioni, Fernanda Carlise

    2010-12-01

    The aim of this research is to describe factors that may influence the constitution of social networks and participation in a community referenced to a Family Health Care Unit, located in a medium-sized city in the South of Brazil. It is a qualitative research developed with key informants, community members, community health agents and other health team personnel. The method used was rapid participative assessment, through semi-structured interviews and field observation. Content analysis was used and two categories emerged: considerations about social networks and community participation. The first category presents factors related to social networks, such as family aggregation, socio-economic structure, alcoholism, among others. The second one presents community organization and the ways people participate in the community. Discussions and reflections presented in this paper enable to conclude that strategies to promote strengthening of bonds and greater mobilization for social participation may be developed.

  9. A Standard Nomenclature for Referencing and Authentication of Pluripotent Stem Cells.

    Science.gov (United States)

    Kurtz, Andreas; Seltmann, Stefanie; Bairoch, Amos; Bittner, Marie-Sophie; Bruce, Kevin; Capes-Davis, Amanda; Clarke, Laura; Crook, Jeremy M; Daheron, Laurence; Dewender, Johannes; Faulconbridge, Adam; Fujibuchi, Wataru; Gutteridge, Alexander; Hei, Derek J; Kim, Yong-Ou; Kim, Jung-Hyun; Kokocinski, Anja Kolb-; Lekschas, Fritz; Lomax, Geoffrey P; Loring, Jeanne F; Ludwig, Tenneille; Mah, Nancy; Matsui, Tohru; Müller, Robert; Parkinson, Helen; Sheldon, Michael; Smith, Kelly; Stachelscheid, Harald; Stacey, Glyn; Streeter, Ian; Veiga, Anna; Xu, Ren-He

    2018-01-09

    Unambiguous cell line authentication is essential to avoid loss of association between data and cells. The risk for loss of references increases with the rapidity that new human pluripotent stem cell (hPSC) lines are generated, exchanged, and implemented. Ideally, a single name should be used as a generally applied reference for each cell line to access and unify cell-related information across publications, cell banks, cell registries, and databases and to ensure scientific reproducibility. We discuss the needs and requirements for such a unique identifier and implement a standard nomenclature for hPSCs, which can be automatically generated and registered by the human pluripotent stem cell registry (hPSCreg). To avoid ambiguities in PSC-line referencing, we strongly urge publishers to demand registration and use of the standard name when publishing research based on hPSC lines. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

  10. A Standard Nomenclature for Referencing and Authentication of Pluripotent Stem Cells

    Directory of Open Access Journals (Sweden)

    Andreas Kurtz

    2018-01-01

    Full Text Available Unambiguous cell line authentication is essential to avoid loss of association between data and cells. The risk for loss of references increases with the rapidity that new human pluripotent stem cell (hPSC lines are generated, exchanged, and implemented. Ideally, a single name should be used as a generally applied reference for each cell line to access and unify cell-related information across publications, cell banks, cell registries, and databases and to ensure scientific reproducibility. We discuss the needs and requirements for such a unique identifier and implement a standard nomenclature for hPSCs, which can be automatically generated and registered by the human pluripotent stem cell registry (hPSCreg. To avoid ambiguities in PSC-line referencing, we strongly urge publishers to demand registration and use of the standard name when publishing research based on hPSC lines.

  11. Peer referencing in adolescent decision making as a function of perceived parenting style.

    Science.gov (United States)

    Bednar, Dell Elaine; Fisher, Terri D

    2003-01-01

    This study examined the relationship between parenting style and adolescent decision making. Two hundred sixty-two college students completed a decision-making scale as well as a parenting scale in an effort to determine if the child-rearing style of their parents was related to the tendency of these late adolescents to reference peers rather than parents or other adults in decision making. The results indicated that adolescents raised by authoritative parents tended to refer to their parents for moral and informational decisions, while adolescents raised by authoritarian, permissive, or neglecting-rejecting parents more often referenced their peers for moral and informational decisions. Adolescents referred to their peers for social decisions regardless of how they were raised. Parental responsiveness was a significant factor in determining the source of adolescent decision-making assistance, but parental demandingness was not. It was concluded that less orientation toward peers during late adolescence seems to be another advantage of authoritative parenting.

  12. Airborne laser scanner aided inertial for terrain referenced navigation in unknown environments

    Science.gov (United States)

    Vadlamani, Ananth Kalyan

    A dead-reckoning terrain referenced navigation (TRN) system that uses airborne laser ranging sensors to aid an aircraft inertial navigation system (INS) is presented. Improved navigation performance is achieved through estimation of vehicle velocity and position using terrain measurements. The system only uses aircraft sensors and simultaneously performs the dual functions of mapping and navigation in unknown environments. The theory, algorithms and results of the system performance are presented using simulations and flight test data. This dissertation focuses primarily on the use of dual airborne laser scanners (ALS) for aiding an INS. Dual ALS measurements are used to generate overlapping terrain models, which are then used to estimate the INS velocity and position errors and constrain its drift. By keeping track of its errors, a navigation-grade INS is aided in a feed-forward manner. This dead-reckoning navigation algorithm is generic enough to be easily extendable to use other optical sensors. Data integrity, sensor alignment and the effects of vegetation noise, attitude and heading accuracy are analyzed. Furthermore, a feedback coupled aiding scheme is presented in which a tactical-grade inertial measurement unit (IMU) is aided with dual ALS measurements by feeding the estimated velocity back into the IMU computations. The proposed system can potentially serve as a backup during temporary Global Positioning System (GPS) signal outages, or it can be used to coast for extended periods of time. Although it has elements of conventional TRN, this system does not require a terrain database since its in-flight mapping capability generates the terrain data for navigation. Hence, the system can be used in both non-GPS as well as unknown terrain environments. The navigation system is dead-reckoning in nature and errors accumulate over time, unless the system can be reset periodically by geo-referenced terrain data or a position estimate from another navigation aid.

  13. Cancer genomics

    DEFF Research Database (Denmark)

    Norrild, Bodil; Guldberg, Per; Ralfkiær, Elisabeth Methner

    2007-01-01

    Almost all cells in the human body contain a complete copy of the genome with an estimated number of 25,000 genes. The sequences of these genes make up about three percent of the genome and comprise the inherited set of genetic information. The genome also contains information that determines when...

  14. Cancer genomics

    DEFF Research Database (Denmark)

    Norrild, Bodil; Guldberg, Per; Ralfkiær, Elisabeth Methner

    2007-01-01

    Almost all cells in the human body contain a complete copy of the genome with an estimated number of 25,000 genes. The sequences of these genes make up about three percent of the genome and comprise the inherited set of genetic information. The genome also contains information that determines whe...

  15. Individual employee's perceptions of " Group-level Safety Climate" (supervisor referenced) versus " Organization-level Safety Climate" (top management referenced): Associations with safety outcomes for lone workers.

    Science.gov (United States)

    Huang, Yueng-Hsiang; Lee, Jin; McFadden, Anna C; Rineer, Jennifer; Robertson, Michelle M

    2017-01-01

    Research has shown that safety climate is among the strongest predictors of safety behavior and safety outcomes in a variety of settings. Previous studies have established that safety climate is a multi-faceted construct referencing multiple levels of management within a company, most generally: the organization level (employee perceptions of top management's commitment to and prioritization of safety) and group level (employee perceptions of direct supervisor's commitment to and prioritization of safety). Yet, no research to date has examined the potential interaction between employees' organization-level safety climate (OSC) and group-level safety climate (GSC) perceptions. Furthermore, prior research has mainly focused on traditional work environments in which supervisors and workers interact in the same location throughout the day. Little research has been done to examine safety climate with regard to lone workers. The present study aims to address these gaps by examining the relationships between truck drivers' (as an example of lone workers) perceptions of OSC and GSC, both potential linear and non-linear relationships, and how these predict important safety outcomes. Participants were 8095 truck drivers from eight trucking companies in the United States with an average response rate of 44.8%. Results showed that employees' OSC and GSC perceptions are highly correlated (r= 0.78), but notable gaps between the two were observed for some truck drivers. Uniquely, both OSC and GSC scores were found to have curvilinear relationships with safe driving behavior, and both scores were equally predictive of safe driving behavior. Results also showed the two levels of climate significantly interacted with one another to predict safety behavior such that if either the OSC or GSC scores were low, the other's contribution to safety behavior became stronger. These findings suggest that OSC and GSC may function in a compensatory manner and promote safe driving behavior even

  16. Referenced Publication Years Spectroscopy applied to iMetrics: Scientometrics, Journal of Informetrics, and a relevant subset of JASIST

    NARCIS (Netherlands)

    Leydesdorff, L.; Bornmann, L.; Marx, W.; Milojević, S.

    2014-01-01

    We have developed a (freeware) routine for "Referenced Publication Years Spectroscopy" (RPYS) and apply this method to the historiography of "iMetrics," that is, the junction of the journals Scientometrics, Informetrics, and the relevant subset of JASIST (approx. 20%) that shapes the intellectual

  17. Imagining School Autonomy in High-Performing Education Systems: East Asia as a Source of Policy Referencing in England

    Science.gov (United States)

    You, Yun; Morris, Paul

    2016-01-01

    Education reform is increasingly based on emulating the features of "world-class" systems that top international attainment surveys and, in England specifically, East Asia is referenced as the "inspiration" for their education reforms. However, the extent to which the features identified by the UK Government accord with the…

  18. BMI-Referenced Cut-Points for Recommended Daily Pedometer-Determined Steps in Australian Children and Adolescents

    Science.gov (United States)

    McCormack, Gavin R.; Rutherford, Jack; Giles-Corti, Billie; Tudor-Locke, Catrine; Bull, Fiona

    2011-01-01

    The purpose of this study was to establish sex-specific criterion-referenced standards for pedometer-determined physical activity related to body mass index (BMI)-defined weight status among youth. We analyzed data from 7-16-year-old boys (n = 338) and girls (n = 337) and used pedometer-assessed physical activity and anthropometric data to derive…

  19. A Brief "DSM-IV"-Referenced Teacher Rating Scale for Monitoring Behavioral Improvement in ADHD and Co-Occurring Symptoms

    Science.gov (United States)

    Sprafkin, Joyce; Mattison, Richard E.; Gadow, Kenneth D.; Schneider, Jayne; Lavigne, John V.

    2011-01-01

    Objective: To examine the psychometric properties of the 30-item teacher's version of the Child and Adolescent Symptom Inventory Progress Monitor (CASI-PM-T), a "DSM-IV"-referenced rating scale for monitoring change in ADHD and co-occurring symptoms in youths receiving behavioral or pharmacological interventions. Method: Three separate studies…

  20. Relationships between Narrative Language Samples and Norm-Referenced Test Scores in Language Assessments of School-Age Children

    Science.gov (United States)

    Ebert, Kerry Danahy; Scott, Cheryl M.

    2014-01-01

    Purpose: Both narrative language samples and norm-referenced language tests can be important components of language assessment for school-age children. The present study explored the relationship between these 2 tools within a group of children referred for language assessment. Method: The study is a retrospective analysis of clinical records from…

  1. Accelerating Preschoolers' Early Literacy Development through Classroom-Based Teacher-Child Storybook Reading and Explicit Print Referencing

    Science.gov (United States)

    Justice, Laura M.; Kaderavek, Joan N.; Fan, Xitao; Sofka, Amy; Hunt, Aileen

    2009-01-01

    Purpose: This study examined the impact of teacher use of a print referencing style during classroom-based storybook reading sessions conducted over an academic year. Impacts on preschoolers' early literacy development were examined, focusing specifically on the domain of print knowledge. Method: This randomized, controlled trial examined the…

  2. DETERMINING PARAMETERS OF THE DIELECTRIC FUNCTION OF A SUBSTANCE IN AQUEOUS SOLUTION BY SELF-REFERENCED REFLECTION THZ SPECTROSCOPY

    DEFF Research Database (Denmark)

    2008-01-01

    Method and apparatus for determining dielectric function of liquid solutions and thereby concentrations of substances in aqueous solution or the volatile/non-volatile nature of the liquid by self-referenced reflection THz spectroscopy. Having the aqueous solution in any container with a window al....... The invention is particularly useful for determining alcohol (ethanol) content in aqueous solution containing other substances and particles....

  3. Measurement of the transverse electric field profile of light by a self-referencing method with direct phase determination.

    Science.gov (United States)

    Bamber, C; Sutherland, B; Patel, A; Stewart, C; Lundeen, J S

    2012-01-30

    We present a method for measuring the transverse electric field profile of a beam of light which allows for direct phase retrieval. The measured values correspond, within a normalization constant, to the real and imaginary parts of the electric field in a plane normal to the direction of propagation. This technique represents a self-referencing method for probing the wavefront characteristics of light.

  4. An Investigation of the Validity of the Sequential Probability Ratio Test for Mastery Decisions in Criterion-Referenced Testing.

    Science.gov (United States)

    Frick, Theodore W.

    The sequential probability ratio test (SPRT), developed by Abraham Wald, is one statistical model available for making mastery decisions during computer-based criterion referenced tests. The predictive validity of the SPRT was empirically investigated with two different and relatively large item pools with heterogeneous item parameters. Graduate…

  5. A hydrologic network supporting spatially referenced regression modeling in the Chesapeake Bay Watershed.

    Science.gov (United States)

    Brakebill, John W; Preston, Stephen D

    2003-01-01

    The U.S. Geological Survey has developed a methodology for statistically relating nutrient sources and land-surface characteristics to nutrient loads of streams. The methodology is referred to as SPAtially Referenced Regressions On Watershed attributes (SPARROW), and relates measured stream nutrient loads to nutrient sources using nonlinear statistical regression models. A spatially detailed digital hydrologic network of stream reaches, stream-reach characteristics such as mean streamflow, water velocity, reach length, and travel time, and their associated watersheds supports the regression models. This network serves as the primary framework for spatially referencing potential nutrient source information such as atmospheric deposition, septic systems, point-sources, land use, land cover, and agricultural sources and land-surface characteristics such as land use, land cover, average-annual precipitation and temperature, slope, and soil permeability. In the Chesapeake Bay watershed that covers parts of Delaware, Maryland, Pennsylvania, New York, Virginia, West Virginia, and Washington D.C., SPARROW was used to generate models estimating loads of total nitrogen and total phosphorus representing 1987 and 1992 land-surface conditions. The 1987 models used a hydrologic network derived from an enhanced version of the U.S. Environmental Protection Agency's digital River Reach File, and course resolution Digital Elevation Models (DEMs). A new hydrologic network was created to support the 1992 models by generating stream reaches representing surface-water pathways defined by flow direction and flow accumulation algorithms from higher resolution DEMs. On a reach-by-reach basis, stream reach characteristics essential to the modeling were transferred to the newly generated pathways or reaches from the enhanced River Reach File used to support the 1987 models. To complete the new network, watersheds for each reach were generated using the direction of surface-water flow derived

  6. A Geo-referenced 3D model of the Juan de Fuca Slab and associated seismicity

    Science.gov (United States)

    Blair, J.L.; McCrory, P.A.; Oppenheimer, D.H.; Waldhauser, F.

    2011-01-01

    We present a Geographic Information System (GIS) of a new 3-dimensional (3D) model of the subducted Juan de Fuca Plate beneath western North America and associated seismicity of the Cascadia subduction system. The geo-referenced 3D model was constructed from weighted control points that integrate depth information from hypocenter locations and regional seismic velocity studies. We used the 3D model to differentiate earthquakes that occur above the Juan de Fuca Plate surface from earthquakes that occur below the plate surface. This GIS project of the Cascadia subduction system supersedes the one previously published by McCrory and others (2006). Our new slab model updates the model with new constraints. The most significant updates to the model include: (1) weighted control points to incorporate spatial uncertainty, (2) an additional gridded slab surface based on the Generic Mapping Tools (GMT) Surface program which constructs surfaces based on splines in tension (see expanded description below), (3) double-differenced hypocenter locations in northern California to better constrain slab location there, and (4) revised slab shape based on new hypocenter profiles that incorporate routine depth uncertainties as well as data from new seismic-reflection and seismic-refraction studies. We also provide a 3D fly-through animation of the model for use as a visualization tool.

  7. Tibia-based referencing for standard proximal tibial radiographs during intramedullary nailing.

    Science.gov (United States)

    Bible, Jesse E; Choxi, Ankeet A; Dhulipala, Sravan C; Evans, Jason M; Mir, Hassan R

    2013-11-01

    Limited information exists to define standard tibial radiographs. The purpose of this study was to define new landmarks on the proximal tibia for standard anteroposterior and lateral radiographs. In 10 cadaveric knees, fibular head bisection was considered the anteroposterior image, and femoral condyle overlap the lateral image. In another 10 knees, a "twin peaks" anteroposterior view, showing the sharpest profile of the tibial spines, was used. The "flat plateau" lateral image was obtained by aligning the femoral condyles then applying a varus adjustment with overlap of the tibial plateaus. Medial peritendinous approaches were performed, and an entry reamer used to open the medullary canal. A priori analysis showed good to excellent intra-/inter-observer reliability with the new technique (intra-class correlation coefficient ICC 0.61-0.90). The "twin peaks" anteroposterior radiograph was externally rotated 2.7±2.1° compared to the standard radiograph with fibular head bisection. Portal position and incidence of damage to intra-articular structures did not significantly differ between groups (P>.05). The "twin peaks" anteroposterior view and "flat plateau" lateral view can safely be used for nail entry portal creation in the anatomic safe zone. Tibia-based radiographic referencing is useful for intramedullary nailing cases in which knee or proximal tibiofibular joint anatomy is altered.

  8. Red light-excitable dual lifetime referenced optical pH sensors with intrinsic temperature compensation.

    Science.gov (United States)

    Borisov, Sergey M; Gatterer, Karl; Klimant, Ingo

    2010-07-01

    Red light-excitable pH sensing materials are manufactured which rely on the use of a fluorescent seminaphthorhodafluor indicator and a luminescent inorganic phosphor as a reference. The phosphors, chromium(III)-activated lanthanide aluminium borates, benefit from chemical and photochemical robustness and are not affected by oxygen. Particularly, a dual lifetime referenced sensing material relies on Cr(III)-activated gadolinium aluminium borate which has low temperature dependence of the decay time. The second material is based on highly temperature-sensitive Cr(III)-doped yttrium aluminium borate and enables dual sensing of pH and temperature. Here, the phosphor simultaneously acts as a temperature probe and as a reference for the pH indicator. The adverse effects of temperature on the properties of the pH indicator are compensated for. The dynamic range of the sensors is optimized by varying the ratio of the components which makes the materials suitable for physiological measurements and for marine applications. The rather poor chemical and photochemical stability of the pH indicator at room temperature should be considered if prolonged measurements are performed.

  9. Comb-referenced frequency-sweeping interferometry for precisely measuring large stepped structures.

    Science.gov (United States)

    Zhang, Weipeng; Wei, Haoyun; Yang, Honglei; Wu, Xuejian; Li, Yan

    2018-02-10

    A precise 3D surface measurement method for large stepped structures without height ambiguity is proposed based on optical-frequency-comb-referenced frequency-sweeping interferometry and Fourier-transformed fractional phase retrieval. Unlike other interferometry that depends on the absolute phase value for several certain wavelengths, this method obtains results from the phase change during frequency sweeping and thus remains free from the confined non-ambiguity range. By reference to an optical frequency comb, the relative uncertainty from the tunable laser frequency was reduced by three orders of magnitude, and the sweeping frequency range can be precisely determined. Besides, the fractional phase can be rapidly retrieved in only one step using a Fourier transform method, with advantages of high accuracy and immunity to light intensity fluctuation and mechanical vibration noise. Samples of step heights from 1 μm to 1 mm were measured, and the standard uncertainty was 45 nm. This permits applications such as quality assurance in microelectronics production and micro-electro-mechanical system (MEMS) manufacture.

  10. Referenced dual pressure- and temperature-sensitive paint for digital color camera read out.

    Science.gov (United States)

    Fischer, Lorenz H; Karakus, Cüneyt; Meier, Robert J; Risch, Nikolaus; Wolfbeis, Otto S; Holder, Elisabeth; Schäferling, Michael

    2012-12-03

    The first fluorescent material for the referenced simultaneous RGB (red green blue) imaging of barometric pressure (oxygen partial pressure) and temperature is presented. This sensitive coating consists of two platinum(II) complexes as indicators and a reference dye, each of which is incorporated in appropriate polymer nanoparticles. These particles are dispersed in a polyurethane hydrogel and spread onto a solid support. The emission of the (oxygen) pressure indicator, PtTFPP, matches the red channel of a RGB color camera, whilst the emission of the temperature indicator [Pt(II) (Br-thq)(acac)] matches the green channel. The reference dye, 9,10-diphenylanthracene, emits in the blue channel. In contrast to other dual-sensitive materials, this new coating allows for the simultaneous imaging of both indicator signals, as well as the reference signal, in one RGB color picture without having to separate the signals with additional optical filters. All of these dyes are excitable with a 405 nm light-emitting diode (LED). With this new composite material, barometric pressure can be determined with a resolution of 22 mbar; the temperature can be determined with a resolution of 4.3 °C. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Pierre Muller's Concept of Referencing Applied to some Forced Displacement Public Policy Instruments in Colombia

    Directory of Open Access Journals (Sweden)

    Carmen Jimena Holguín

    2017-01-01

    Full Text Available This text presents how Pierre Muller's concept of public policy referencing is applied to some public policy instruments as analyzed during the 1994 - 2014 period when caring for displaced population. This period allowed the observation of an emergence of a series of images when caring for the displaced that, seen as a whole, make visible the complexity of this phenomenon in terms of public policy. This insofar as how it shows that discourses and actions when caring for the displaced population lack continuity even during the term of the incumbent government, which complicates the caring and restitution of rights processes. The changes in the reference frame (i.e. the collective imagination when caring for displaced population that resulted from the analysis: from a perspective of harm (CONPES 2804 dated 1995, to one of differential care (CONPES 2924 dated 1997; Then to one of specialized care (Law 387 dated 1997, to finally arrive at one of differential care (Law 1448 dated 2011.

  12. GEO-REFERENCED MAPPING USING AN AIRBORNE 3D TIME-OF-FLIGHT CAMERA

    Directory of Open Access Journals (Sweden)

    T. K. Kohoutek

    2012-09-01

    Full Text Available This paper presents the first experience of a close range bird's eye view photogrammetry with range imaging (RIM sensors for the real time generation of high resolution geo-referenced 3D surface models. The aim of this study was to develop a mobile, versatile and less costly outdoor survey methodology to measure natural surfaces compared to the terrestrial laser scanning (TLS. Two commercial RIM cameras (SR4000 by MESA Imaging AG and a CamCube 2.0 by PMDTechnologies GmbH were mounted on a lightweight crane and on an unmanned aerial vehicle (UAV. The field experiments revealed various challenges in real time deployment of the two state-of-the-art RIM systems, e.g. processing of the large data volume. Acquisition strategy and data processing and first measurements are presented. The precision of the measured distances is less than 1 cm for good conditions. However, the measurement precision degraded under the test conditions due to direct sunlight, strong illumination contrasts and helicopter vibrations.

  13. BIBLIOGRAPHIC STUDY IN RISK MANAGEMENT AIMED TO IDENTIFY MORE REFERENCED TOOLS, METHODS AND RELATIONSHIPS

    Directory of Open Access Journals (Sweden)

    Alamir Costa Louro

    2015-06-01

    Full Text Available The objective of this paper is to identify and discuss trends in tools and methods used in project risk management and its relationship to other matters, using current scientific articles. The focus isn´t in understanding how they work in technical terms, but think about the possibilities of deepening in academic studies, including making several suggestions for future research. Adjacent to the article there is a discussion about an alleged "one best way" imperative normativity approach. It was answered the following research questions: what subjects and theories are related to project risk management tools and methods? The first contribution is related to the importance of the academic Chris Chapman as an author who has more published and also more referenced in the survey. There are several contributions on various subjects such as: the perception of the existence of many conceptual papers; papers about construction industry, problematization of contracts according to agency theory, IT and ERPs issues. Other contributions came from the bibliometric method that brings lot of consolidated information about terms, topics, authors, references, periods and, of course, methods and tools about Project Risk Management.

  14. Hard X-ray Fourier transform holography from an array of oriented referenced objects.

    Science.gov (United States)

    Iwamoto, Hiroyuki; Yagi, Naoto

    2011-07-01

    Hard X-ray Fourier transform holography (HXFTH) is a promising method for imaging nanoscale objects, including biological molecules, with a spatial resolution of a nanometer or better. However, it suffers from low scattering intensities being available for imaging owing to smaller object size and the low scattering cross section inherent in hard X-rays. One technique to overcome the problem would be to use an array of oriented objects, each with its own reference. Here the feasibility of this approach was experimentally tested by recording diffraction patterns from nanofabricated test patterns arranged in a 5 × 5 matrix. At an X-ray energy of 8 keV (λ = 1.55 Å), the image of the original test pattern was clearly restored with 60 s exposure on an imaging plate; the image was still recognizable with a 500 ms exposure on a CCD detector at the BL40XU beamline at SPring-8. The results demonstrate that the use of an array of referenced oriented objects for HXFTH is workable, and that it can be considered as a practical candidate for imaging biological molecules, identical particles of which are available but diffract even more weakly than artificially fabricated test patterns.

  15. A Brightness-Referenced Star Identification Algorithm for APS Star Trackers

    Science.gov (United States)

    Zhang, Peng; Zhao, Qile; Liu, Jingnan; Liu, Ning

    2014-01-01

    Star trackers are currently the most accurate spacecraft attitude sensors. As a result, they are widely used in remote sensing satellites. Since traditional charge-coupled device (CCD)-based star trackers have a limited sensitivity range and dynamic range, the matching process for a star tracker is typically not very sensitive to star brightness. For active pixel sensor (APS) star trackers, the intensity of an imaged star is valuable information that can be used in star identification process. In this paper an improved brightness referenced star identification algorithm is presented. This algorithm utilizes the k-vector search theory and adds imaged stars' intensities to narrow the search scope and therefore increase the efficiency of the matching process. Based on different imaging conditions (slew, bright bodies, etc.) the developed matching algorithm operates in one of two identification modes: a three-star mode, and a four-star mode. If the reference bright stars (the stars brighter than three magnitude) show up, the algorithm runs the three-star mode and efficiency is further improved. The proposed method was compared with other two distinctive methods the pyramid and geometric voting methods. All three methods were tested with simulation data and actual in orbit data from the APS star tracker of ZY-3. Using a catalog composed of 1500 stars, the results show that without false stars the efficiency of this new method is 4∼5 times that of the pyramid method and 35∼37 times that of the geometric method. PMID:25299950

  16. Measurement of M2-Curve for Asymmetric Beams by Self-Referencing Interferometer Wavefront Sensor

    Directory of Open Access Journals (Sweden)

    Yongzhao Du

    2016-11-01

    Full Text Available For asymmetric laser beams, the values of beam quality factor M x 2 and M y 2 are inconsistent if one selects a different coordinate system or measures beam quality with different experimental conditionals, even when analyzing the same beam. To overcome this non-uniqueness, a new beam quality characterization method named as M2-curve is developed. The M2-curve not only contains the beam quality factor M x 2 and M y 2 in the x-direction and y-direction, respectively; but also introduces a curve of M x α 2 versus rotation angle α of coordinate axis. Moreover, we also present a real-time measurement method to demonstrate beam propagation factor M2-curve with a modified self-referencing Mach-Zehnder interferometer based-wavefront sensor (henceforth SRI-WFS. The feasibility of the proposed method is demonstrated with the theoretical analysis and experiment in multimode beams. The experimental results showed that the proposed measurement method is simple, fast, and a single-shot measurement procedure without movable parts.

  17. Comparative Genomics

    Indian Academy of Sciences (India)

    An important hallmark of biological research is the aspect of 'comparisons'. As the complete genome sequences of numerous organisms have become available, the emphasis in biology has shifted to comparisons at the genome level. Indeed, the last few years have witnessed an exponential rise in the number of ...

  18. Comparative Genomics

    Indian Academy of Sciences (India)

    structions of the tree of life, drug discovery programs, func- tion predictions of hypothetical proteins and genes, regula- tory motifs and other non-coding DNA motifs, and genome ... expertise in assembling sequences. Beginning with the complete genome sequence of the bacterial pathogen Haemophilus influenzae that was ...

  19. New Contemporary Criterion-Referenced Assessment Instruments for Astronomy & Geology: TOAST & EGGS

    Science.gov (United States)

    Guffey, Sarah Katie; Slater, Stephanie J.; Slater, Timothy F.

    2015-08-01

    Considerable effort in the astronomy and Earth sciences education research over the past decade has focused on developing assessment tools in the form of multiple-choice conceptual diagnostics and content knowledge surveys. This has been critically important in advancing discipline-based education research allowing scholar to establish the initial, incoming knowledge state of students as well as to attempt to measure some of the impacts of innovative instructional interventions. Before now, few of the existing instruments were constructed upon a solid list of clearly articulated and widely agreed upon learning objectives. Whereas first-generation assessment tools, such as the Astronomy Diagnostics Test ADT2) were based primarily upon further identifying documented astronomy misconceptions, scholars from the CAPER Center for Astronomy & Physics Education Research team are creating contemporary instruments based instead by developing items using modern test construction techniques and tightly aligned to the consensus learning goals identified by the American Association of the Advancement of Science’s Project 2061 Benchmarks, and the National Research Council’s National Science Education Standards, and the National Research Council’s Frameworks for A Framework for K-12 Science Education: Practices, Crosscutting Concepts, and Core Ideas. These consensus learning goals are further enhanced guiding documents from the American Astronomical Society - Chair’s Conference on ASTRO 101 and the NSF-funded Earth Science Literacy Initiative. Two of the resulting criterion-referenced assessment tools widely used by researchers are the Test Of Astronomy STandards (TOAST) and the Exam of GeoloGy StandardS (EGGS). These easy-to-use and easy-to-score multiple-choice instruments have a high degree of reliability and validity for instructors and researchers needing information on students’ initial knowledge state at the beginning of a course and can be used, in aggregate, to

  20. Impact of External Price Referencing on Medicine Prices – A Price Comparison Among 14 European Countries

    Science.gov (United States)

    Leopold, Christine; Mantel-Teeuwisse, Aukje Katja; Seyfang, Leonhard; Vogler, Sabine; de Joncheere, Kees; Laing, Richard Ogilvie; Leufkens, Hubert

    2012-01-01

    Objectives: This study aims to examine the impact of external price referencing (EPR) on on-patent medicine prices, adjusting for other factors that may affect price levels such as sales volume, exchange rates, gross domestic product (GDP) per capita, total pharmaceutical expenditure (TPE), and size of the pharmaceutical industry. Methods: Price data of 14 on-patent products, in 14 European countries in 2007 and 2008 were obtained from the Pharmaceutical Price Information Service of the Austrian Health Institute. Based on the unit ex-factory prices in EURO, scaled ranks per country and per product were calculated. For the regression analysis the scaled ranks per country and product were weighted; each country had the same sum of weights but within a country the weights were proportional to its sales volume in the year (data obtained from IMS Health). Taking the scaled ranks, several statistical analyses were performed by using the program “R”, including a multiple regression analysis (including variables such as GDP per capita and national industry size). Results: This study showed that on average EPR as a pricing policy leads to lower prices. However, the large variation in price levels among countries using EPR confirmed that the price level is not only driven by EPR. The unadjusted linear regression model confirms that applying EPR in a country is associated with a lower scaled weighted rank (p=0.002). This interaction persisted after inclusion of total pharmaceutical expenditure per capita and GDP per capita in the final model. Conclusions: The study showed that for patented products, prices are in general lower in case the country applied EPR. Nevertheless substantial price differences among countries that apply EPR could be identified. Possible explanations could be found through a correlation between pharmaceutical industry and the scaled price ranks. In conclusion, we found that implementing external reference pricing could lead to lower prices. PMID

  1. Integrated GNSS attitude determination and positioning for direct geo-referencing.

    Science.gov (United States)

    Nadarajah, Nandakumaran; Paffenholz, Jens-André; Teunissen, Peter J G

    2014-07-17

    Direct geo-referencing is an efficient methodology for the fast acquisition of 3D spatial data. It requires the fusion of spatial data acquisition sensors with navigation sensors, such as Global Navigation Satellite System (GNSS) receivers. In this contribution, we consider an integrated GNSS navigation system to provide estimates of the position and attitude (orientation) of a 3D laser scanner. The proposed multi-sensor system (MSS) consists of multiple GNSS antennas rigidly mounted on the frame of a rotating laser scanner and a reference GNSS station with known coordinates. Precise GNSS navigation requires the resolution of the carrier phase ambiguities. The proposed method uses the multivariate constrained integer least-squares (MC-LAMBDA) method for the estimation of rotating frame ambiguities and attitude angles. MC-LAMBDA makes use of the known antenna geometry to strengthen the underlying attitude model and, hence, to enhance the reliability of rotating frame ambiguity resolution and attitude determination. The reliable estimation of rotating frame ambiguities is consequently utilized to enhance the relative positioning of the rotating frame with respect to the reference station. This integrated (array-aided) method improves ambiguity resolution, as well as positioning accuracy between the rotating frame and the reference station. Numerical analyses of GNSS data from a real-data campaign confirm the improved performance of the proposed method over the existing method. In particular, the integrated method yields reliable ambiguity resolution and reduces position standard deviation by a factor of about 0:8, matching the theoretical gain of √ 3/4 for two antennas on the rotating frame and a single antenna at the reference station.

  2. Bird radar validation in the field by time-referencing line-transect surveys.

    Science.gov (United States)

    Dokter, Adriaan M; Baptist, Martin J; Ens, Bruno J; Krijgsveld, Karen L; van Loon, E Emiel

    2013-01-01

    Track-while-scan bird radars are widely used in ornithological studies, but often the precise detection capabilities of these systems are unknown. Quantification of radar performance is essential to avoid observational biases, which requires practical methods for validating a radar's detection capability in specific field settings. In this study a method to quantify the detection capability of a bird radar is presented, as well a demonstration of this method in a case study. By time-referencing line-transect surveys, visually identified birds were automatically linked to individual tracks using their transect crossing time. Detection probabilities were determined as the fraction of the total set of visual observations that could be linked to radar tracks. To avoid ambiguities in assigning radar tracks to visual observations, the observer's accuracy in determining a bird's transect crossing time was taken into account. The accuracy was determined by examining the effect of a time lag applied to the visual observations on the number of matches found with radar tracks. Effects of flight altitude, distance, surface substrate and species size on the detection probability by the radar were quantified in a marine intertidal study area. Detection probability varied strongly with all these factors, as well as species-specific flight behaviour. The effective detection range for single birds flying at low altitude for an X-band marine radar based system was estimated at ~1.5 km. Within this range the fraction of individual flying birds that were detected by the radar was 0.50 ± 0.06 with a detection bias towards higher flight altitudes, larger birds and high tide situations. Besides radar validation, which we consider essential when quantification of bird numbers is important, our method of linking radar tracks to ground-truthed field observations can facilitate species-specific studies using surveillance radars. The methodology may prove equally useful for optimising

  3. Bird radar validation in the field by time-referencing line-transect surveys.

    Directory of Open Access Journals (Sweden)

    Adriaan M Dokter

    Full Text Available Track-while-scan bird radars are widely used in ornithological studies, but often the precise detection capabilities of these systems are unknown. Quantification of radar performance is essential to avoid observational biases, which requires practical methods for validating a radar's detection capability in specific field settings. In this study a method to quantify the detection capability of a bird radar is presented, as well a demonstration of this method in a case study. By time-referencing line-transect surveys, visually identified birds were automatically linked to individual tracks using their transect crossing time. Detection probabilities were determined as the fraction of the total set of visual observations that could be linked to radar tracks. To avoid ambiguities in assigning radar tracks to visual observations, the observer's accuracy in determining a bird's transect crossing time was taken into account. The accuracy was determined by examining the effect of a time lag applied to the visual observations on the number of matches found with radar tracks. Effects of flight altitude, distance, surface substrate and species size on the detection probability by the radar were quantified in a marine intertidal study area. Detection probability varied strongly with all these factors, as well as species-specific flight behaviour. The effective detection range for single birds flying at low altitude for an X-band marine radar based system was estimated at ~1.5 km. Within this range the fraction of individual flying birds that were detected by the radar was 0.50 ± 0.06 with a detection bias towards higher flight altitudes, larger birds and high tide situations. Besides radar validation, which we consider essential when quantification of bird numbers is important, our method of linking radar tracks to ground-truthed field observations can facilitate species-specific studies using surveillance radars. The methodology may prove equally useful

  4. AIDE Project: Deliverable D5.5 (Software Library for Context-sensitive voice semantic recognition) and referenced documents

    OpenAIRE

    Amat, Guillermo

    2017-01-01

    This publication includes the Deliverable 9.5 (Software Library for Context-sensitive voice semantic recognition) of the AIDE Project (G.A.645322) and the following documents that are referenced in the deliverable: [1] Zed AIDE Research & Development Team (2016). Indoor Mapping Guide. [2] Zed AIDE Research & Development Team (2016). AIDE Location Services. [3] Zed AIDE Research & Development Team (2016). AIDE YARP Wrapper for Location Services. [4] Zed AIDE Research ...

  5. Geo-referenced modelling of metal concentrations in river basins at the catchment scale

    Science.gov (United States)

    Hüffmeyer, N.; Berlekamp, J.; Klasmeier, J.

    2009-04-01

    1. Introduction The European Water Framework Directive demands the good ecological and chemical state of surface waters [1]. This implies the reduction of unwanted metal concentrations in surface waters. To define reasonable environmental target values and to develop promising mitigation strategies a detailed exposure assessment is required. This includes the identification of emission sources and the evaluation of their effect on local and regional surface water concentrations. Point source emissions via municipal or industrial wastewater that collect metal loads from a wide variety of applications and products are important anthropogenic pathways into receiving waters. Natural background and historical influences from ore-mining activities may be another important factor. Non-point emissions occur via surface runoff and erosion from drained land area. Besides deposition metals can be deposited by fertilizer application or the use of metal products such as wires or metal fences. Surface water concentrations vary according to the emission strength of sources located nearby and upstream of the considered location. A direct link between specific emission sources and pathways on the one hand and observed concentrations can hardly be established by monitoring alone. Geo-referenced models such as GREAT-ER (Geo-referenced Regional Exposure Assessment Tool for European Rivers) deliver spatially resolved concentrations in a whole river basin and allow for evaluating the causal relationship between specific emissions and resulting concentrations. This study summarizes the results of investigations for the metals zinc and copper in three German catchments. 2. The model GREAT-ER The geo-referenced model GREAT-ER has originally been developed to simulate and assess chemical burden of European river systems from multiple emission sources [2]. Emission loads from private households and rainwater runoff are individually estimated based on average consumption figures, runoff rates

  6. Cardiovascular genomics.

    Science.gov (United States)

    Wung, Shu-Fen; Hickey, Kathleen T; Taylor, Jacquelyn Y; Gallek, Matthew J

    2013-03-01

    This article provides an update on cardiovascular genomics using three clinically relevant exemplars, including myocardial infarction (MI) and coronary artery disease (CAD), stroke, and sudden cardiac death (SCD). ORGANIZATIONAL CONSTRUCT: Recent advances in cardiovascular genomic research, testing, and clinical implications are presented. Genomic nurse experts reviewed and summarized recent salient literature to provide updates on three selected cardiovascular genomic conditions. Research is ongoing to discover comprehensive genetic markers contributing to many common forms of cardiovascular disease (CVD), including MI and stroke. However, genomic technologies are increasingly being used clinically, particularly in patients with long QT syndrome (LQTS) or hypertrophic cardiomyopathy (HCM) who are at risk for SCD. Currently, there are no clinically recommended genetic tests for many common forms of CVD even though direct-to-consumer genetic tests are being marketed to healthcare providers and the general public. On the other hand, genetic testing for patients with certain single gene conditions, including channelopathies (e.g., LQTS) and cardiomyopathies (e.g., HCM), is recommended clinically. Nurses play a pivotal role in cardiogenetics and are actively engaged in direct clinical care of patients and families with a wide variety of heritable conditions. It is important for nurses to understand current development of cardiovascular genomics and be prepared to translate the new genomic knowledge into practice. © 2013 Sigma Theta Tau International.

  7. Genomic Imprinting

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 5; Issue 9. Genomic Imprinting - Some Interesting Implications for the Evolution of Social Behaviour. Raghavendra Gadagkar. General Article Volume 5 Issue 9 September 2000 pp 58-68 ...

  8. Geo-referenced social accounting with application to integrated watershed planning in the Hudson River Valley

    Science.gov (United States)

    Nowosielski, Audra Ann

    Changing economic activity and patterns of human habitation have long been a cause of concern for the ecological health of the Hudson River and its tributaries. Today, economic development in the Hudson River Valley is often characterized as a battle between proponents of economy-wide growth and citizen groups concerned about the cumulative impact of incremental development on the watershed. Current development trends in the Hudson River Valley are driving the conversion of rural, agricultural and forestland to urban or industrial uses. This thesis is part of a larger study of the economic changes that lead to land use and environmental changes. It focuses specifically on the economic drivers of development in Dutchess County, an area of the lower watershed on the east bank of the Hudson, midway between New York City and the state capital of Albany. The objective was to engage the Dutchess County planning community in developing a planning model, the economic portion of which characterizes the economy with a Social Accounting Matrix (SAM) referenced to a Geographical Information System (GIS). The model was used to assess economic impacts of locally relevant development scenarios including a new IBM semiconductor plant, agro-tourism, and commuting behavior. These scenarios each discuss economic changes that have land use consequences. For example, a new IBM plant will likely instigate new residential development, agro-tourism offers a way to keep land in agricultural use, and the study of commuting behavior leads to insights on how residential growth may depend on commuting patterns, as well as information on the effects of second home communities. The final model will help stakeholders to visualize not only how economic shocks will change their communities, but also how these changes may lead to land use and cumulative environmental impact. Stakeholders will be able to visualize the trade-off between new economic growth and the possible loss of environmental

  9. Geoinformation web-system for processing and visualization of large archives of geo-referenced data

    Science.gov (United States)

    Gordov, E. P.; Okladnikov, I. G.; Titov, A. G.; Shulgina, T. M.

    2010-12-01

    Developed working model of information-computational system aimed at scientific research in area of climate change is presented. The system will allow processing and analysis of large archives of geophysical data obtained both from observations and modeling. Accumulated experience of developing information-computational web-systems providing computational processing and visualization of large archives of geo-referenced data was used during the implementation (Gordov et al, 2007; Okladnikov et al, 2008; Titov et al, 2009). Functional capabilities of the system comprise a set of procedures for mathematical and statistical analysis, processing and visualization of data. At present five archives of data are available for processing: 1st and 2nd editions of NCEP/NCAR Reanalysis, ECMWF ERA-40 Reanalysis, JMA/CRIEPI JRA-25 Reanalysis, and NOAA-CIRES XX Century Global Reanalysis Version I. To provide data processing functionality a computational modular kernel and class library providing data access for computational modules were developed. Currently a set of computational modules for climate change indices approved by WMO is available. Also a special module providing visualization of results and writing to Encapsulated Postscript, GeoTIFF and ESRI shape files was developed. As a technological basis for representation of cartographical information in Internet the GeoServer software conforming to OpenGIS standards is used. Integration of GIS-functionality with web-portal software to provide a basis for web-portal’s development as a part of geoinformation web-system is performed. Such geoinformation web-system is a next step in development of applied information-telecommunication systems offering to specialists from various scientific fields unique opportunities of performing reliable analysis of heterogeneous geophysical data using approved computational algorithms. It will allow a wide range of researchers to work with geophysical data without specific programming

  10. [Nutrition genomics].

    Science.gov (United States)

    Sedová, L; Seda, O

    2004-01-01

    The importance of nutrition for human health and its influence on the onset and course of many diseases are nowadays considered as proven. Only the recent development of molecular biology and biochemical methods allows the elucidation of the molecular mechanisms of diet constituent actions and their subsequent effect on homeostatic mechanisms in health and disease states. The availability of the draft human genome sequence as well as the genome sequences of model organisms, combined with the functional and integrative genomics approaches of systems biology, bring about the possibility to identify alleles and haplotypes responsible for specific reaction to the dietary challenge in susceptible individuals. Such complex interactions are studied within the newly conceived field, the nutrition genomics (nutrigenomics). Using the tools of highly parallel analyses of transcriptome, proteome and metabolome, the nutrition genomics pursues its ultimate goal, i.e. the individualized diet, respecting not only quantitative and qualitative nutritional needs and the actual health status, but also the genetic predispositions of an individual. This approach should lead to prevention of the onset of such diseases as obesity, hypertension or type 2 diabetes, or enhance the efficiency of their therapy.

  11. Marine genomics

    DEFF Research Database (Denmark)

    Oliveira Ribeiro, Ângela Maria; Foote, Andrew David; Kupczok, Anne

    2017-01-01

    evolutionary biology of non-model organisms to species of commercial relevance for fishing, aquaculture and biomedicine. Instead of providing an exhaustive list of available genomic data, we rather set to present contextualized examples that best represent the current status of the field of marine genomics.......Marine ecosystems occupy 71% of the surface of our planet, yet we know little about their diversity. Although the inventory of species is continually increasing, as registered by the Census of Marine Life program, only about 10% of the estimated two million marine species are known. This lag......-throughput sequencing approaches have been helping to improve our knowledge of marine biodiversity, from the rich microbial biota that forms the base of the tree of life to a wealth of plant and animal species. In this review, we present an overview of the applications of genomics to the study of marine life, from...

  12. Listeria Genomics

    Science.gov (United States)

    Cabanes, Didier; Sousa, Sandra; Cossart, Pascale

    The opportunistic intracellular foodborne pathogen Listeria monocytogenes has become a paradigm for the study of host-pathogen interactions and bacterial adaptation to mammalian hosts. Analysis of L. monocytogenes infection has provided considerable insight into how bacteria invade cells, move intracellularly, and disseminate in tissues, as well as tools to address fundamental processes in cell biology. Moreover, the vast amount of knowledge that has been gathered through in-depth comparative genomic analyses and in vivo studies makes L. monocytogenes one of the most well-studied bacterial pathogens. This chapter provides an overview of progress in the exploration of genomic, transcriptomic, and proteomic data in Listeria spp. to understand genome evolution and diversity, as well as physiological aspects of metabolism used by bacteria when growing in diverse environments, in particular in infected hosts.

  13. Noninvasive referencing of intraocular tumors for external beam radiation therapy using optical coherence tomography: A proof of concept

    International Nuclear Information System (INIS)

    Rüegsegger, Michael B.; Steiner, Patrick; Kowal, Jens H.; Geiser, Dominik; Pica, Alessia; Aebersold, Daniel M.

    2014-01-01

    Purpose: External beam radiation therapy is currently considered the most common treatment modality for intraocular tumors. Localization of the tumor and efficient compensation of tumor misalignment with respect to the radiation beam are crucial. According to the state of the art procedure, localization of the target volume is indirectly performed by the invasive surgical implantation of radiopaque clips or is limited to positioning the head using stereoscopic radiographies. This work represents a proof-of-concept for direct and noninvasive tumor referencing based on anterior eye topography acquired using optical coherence tomography (OCT). Methods: A prototype of a head-mounted device has been developed for automatic monitoring of tumor position and orientation in the isocentric reference frame for LINAC based treatment of intraocular tumors. Noninvasive tumor referencing is performed with six degrees of freedom based on anterior eye topography acquired using OCT and registration of a statistical eye model. The proposed prototype was tested based on enucleated pig eyes and registration accuracy was measured by comparison of the resulting transformation with tilt and torsion angles manually induced using a custom-made test bench. Results: Validation based on 12 enucleated pig eyes revealed an overall average registration error of 0.26 ± 0.08° in 87 ± 0.7 ms for tilting and 0.52 ± 0.03° in 94 ± 1.4 ms for torsion. Furthermore, dependency of sampling density on mean registration error was quantitatively assessed. Conclusions: The tumor referencing method presented in combination with the statistical eye model introduced in the past has the potential to enable noninvasive treatment and may improve quality, efficacy, and flexibility of external beam radiotherapy of intraocular tumors

  14. Near-real-time feedback control system for liver thermal ablations based on self-referenced temperature imaging

    International Nuclear Information System (INIS)

    Keserci, Bilgin M.; Kokuryo, Daisuke; Suzuki, Kyohei; Kumamoto, Etsuko; Okada, Atsuya; Khankan, Azzam A.; Kuroda, Kagayaki

    2006-01-01

    Our challenge was to design and implement a dedicated temperature imaging feedback control system to guide and assist in a thermal liver ablation procedure in a double-donut 0.5T open MR scanner. This system has near-real-time feedback capability based on a newly developed 'self-referenced' temperature imaging method using 'moving-slab' and complex-field-fitting techniques. Two phantom validation studies and one ex vivo experiment were performed to compare the newly developed self-referenced method with the conventional subtraction method and evaluate the ability of the feedback control system in the same MR scanner. The near-real-time feedback system was achieved by integrating the following primary functions: (1) imaging of the moving organ temperature; (2) on-line needle tip tracking; (3) automatic turn-on/off the heating devices; (4) a Windows operating system-based novel user-interfaces. In the first part of the validation studies, microwave heating was applied in an agar phantom using a fast spoiled gradient recalled echo in a steady state sequence. In the second part of the validation and ex vivo study, target visualization, treatment planning and monitoring, and temperature and thermal dose visualization with the graphical user interface of the thermal ablation software were demonstrated. Furthermore, MR imaging with the 'self-referenced' temperature imaging method has the ability to localize the hot spot in the heated region and measure temperature elevation during the experiment. In conclusion, we have demonstrated an interactively controllable feedback control system that offers a new method for the guidance of liver thermal ablation procedures, as well as improving the ability to assist ablation procedures in an open MR scanner

  15. Soliton trapping and comb self-referencing in a single microresonator with χ(2) and χ(3) nonlinearities.

    Science.gov (United States)

    Xue, Xiaoxiao; Zheng, Xiaoping; Weiner, Andrew M

    2017-10-15

    A shaped doublet pump pulse is proposed for a simultaneous octave-spanning soliton Kerr frequency comb generation and second-harmonic conversion in a single microresonator. The temporal soliton in the cavity is trapped atop a doublet-pulse pedestal, resulting in a greatly expanded soliton region compared to that with a general Gaussian pulse pump. The possibility of single-microresonator comb self-referencing in a single silicon nitride microring that can facilitate compact on-chip optical clocks is demonstrated via simulation.

  16. A self-referenced reflectance sensor for the detection of lead and other heavy metal ions using optical fibres

    International Nuclear Information System (INIS)

    Guillemain, H; Rajarajan, M; Sun, T; Grattan, K T V

    2009-01-01

    A self-referenced optical fibre sensor for monitoring heavy metals, especially lead, has been developed and evaluated and the results obtained are discussed in detail in this paper. The sensor probe builds on concepts in prior work, creating a small, compact and portable device using an indicator immobilized at the fibre end. It functions in the visible part of the spectrum where the attenuation caused by fibre transmission is small and it offers a possible solution to the need for devices to be used in the field. This represents on-going research where the factors affecting the probe design and immobilization procedure used are considered and solutions offered

  17. Cephalopod genomics

    DEFF Research Database (Denmark)

    Albertin, Caroline B.; Bonnaud, Laure; Brown, C. Titus

    2012-01-01

    The Cephalopod Sequencing Consortium (CephSeq Consortium) was established at a NESCent Catalysis Group Meeting, ``Paths to Cephalopod Genomics-Strategies, Choices, Organization,'' held in Durham, North Carolina, USA on May 24-27, 2012. Twenty-eight participants representing nine countries (Austri...... in this white paper......., Australia, China, Denmark, France, Italy, Japan, Spain and the USA) met to address the pressing need for genome sequencing of cephalopod mollusks. This group, drawn from cephalopod biologists, neuroscientists, developmental and evolutionary biologists, materials scientists, bioinformaticians and researchers...

  18. Genome Imprinting

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 5; Issue 9. Genome Imprinting - The Silencing of ... General Article Volume 5 Issue 9 September 2000 pp 49-57 ... M T Tanuja1. Drosophila Stock Centre, Department of Studies in Zoology, University of Mysore Manasagangotri Mysore 570 006, India.

  19. Genome Imprinting

    Indian Academy of Sciences (India)

    ring pathological condition cystic fibrosis is due to inheritance of both copies of chromosome 7 from the mother. Similarly,. Prader-Willi syndrome in humans is due to the inheritance of both copies of chromosome 15 from the mother. Human Triploids. The triploid (Le. 3 copies of the haploid genome are present instead of the ...

  20. genome editing

    Indian Academy of Sciences (India)

    2016-02-11

    Feb 11, 2016 ... What history tells us. XL. The success story of the expression 'genome editing'. MICHEL MORANGE. Centre Cavaillès, République des Savoirs: Lettres, Sciences, Philosophie USR 3608, Ecole. Normale Supérieure, 29 Rue d'Ulm, 75230, Paris Cedex 05, France. (Fax, 33-144-323941; Email, ...

  1. Ancient genomics

    DEFF Research Database (Denmark)

    Der Sarkissian, Clio; Allentoft, Morten Erik; Avila Arcos, Maria del Carmen

    2015-01-01

    The past decade has witnessed a revolution in ancient DNA (aDNA) research. Although the field's focus was previously limited to mitochondrial DNA and a few nuclear markers, whole genome sequences from the deep past can now be retrieved. This breakthrough is tightly connected to the massive sequen...

  2. Comparative Genomics

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 11; Issue 8. Comparative Genomics - A Powerful New Tool in Biology. Anand K Bachhawat. General Article Volume 11 Issue 8 August 2006 pp 22-40. Fulltext. Click here to view fulltext PDF. Permanent link:

  3. Empirical correlation between protein backbone 15N and 13C secondary chemical shifts and its application to nitrogen chemical shift re-referencing

    International Nuclear Information System (INIS)

    Wang Liya; Markley, John L.

    2009-01-01

    The linear analysis of chemical shifts (LACS) has provided a robust method for identifying and correcting 13 C chemical shift referencing problems in data from protein NMR spectroscopy. Unlike other approaches, LACS does not require prior knowledge of the three-dimensional structure or inference of the secondary structure of the protein. It also does not require extensive assignment of the NMR data. We report here a way of extending the LACS approach to 15 N NMR data from proteins, so as to enable the detection and correction of inconsistencies in chemical shift referencing for this nucleus. The approach is based on our finding that the secondary 15 N chemical shift of the backbone nitrogen atom of residue i is strongly correlated with the secondary chemical shift difference (experimental minus random coil) between the alpha and beta carbons of residue i - 1. Thus once alpha and beta 13 C chemical shifts are available (their difference is referencing error-free), the 15 N referencing can be validated, and an appropriate offset correction can be derived. This approach can be implemented prior to a structure determination and can be used to analyze potential referencing problems in database data not associated with three-dimensional structure. Application of the LACS algorithm to the current BMRB protein chemical shift database, revealed that nearly 35% of the BMRB entries have δ 15 N values mis-referenced by over 0.7 ppm and over 25% of them have δ 1 H N values mis-referenced by over 0.12 ppm. One implication of the findings reported here is that a backbone 15 N chemical shift provides a better indicator of the conformation of the preceding residue than of the residue itself

  4. Self-referenced refractive index sensing with hybrid-Tamm-plasmon-polariton modes in sub-wavelength analyte layers

    Science.gov (United States)

    Kumar, Samir; Shukla, Mukesh Kumar; Sona Maji, Partha; Das, Ritwick

    2017-09-01

    A coupled Tamm-plasmon-polariton (TPP) hybrid-mode based self-referenced refractive-index sensor is proposed. The geometry is comprised of a sub-wavelength analyte (sensing) layer sandwiched between two metal-clad distributed-Bragg-reflectors (DBRs). Reflection spectrum of the geometry exhibits two discernible reflectivity minima within the photonic-bandgap of DBR. The reflectivity minima are essentially due to excitation of two hybrid modes which have symmetric and anti-symmetric field distribution about the center resulting in an anti-crossing behaviour exhibited by hybrid-TPP mode dispersion curves. The low frequency symmetric mode exhibits strong dispersive properties by virtue of significant presence of mode-field in sensing medium. On the other hand, the high-frequency anti-symmetric mode remains unchanged with alterations in sensing layer. Thus, we propose a self-referenced sensing scheme using hybrid-TPP modes with sensitivity varying from 65~nm~RIU-1 to 180~nm~RIU-1 in the visible band. In addition, the TPP resonance are appreciably sharp as compared to surface-plasmon based geometries which results in improved detection accuracy and figure of merit. We also present an analysis for optimizing the sensor design for enhancing the sensitivity as well as detection accuracy.

  5. Personal genomics services: whose genomes?

    Science.gov (United States)

    Gurwitz, David; Bregman-Eschet, Yael

    2009-07-01

    New companies offering personal whole-genome information services over the internet are dynamic and highly visible players in the personal genomics field. For fees currently ranging from US$399 to US$2500 and a vial of saliva, individuals can now purchase online access to their individual genetic information regarding susceptibility to a range of chronic diseases and phenotypic traits based on a genome-wide SNP scan. Most of the companies offering such services are based in the United States, but their clients may come from nearly anywhere in the world. Although the scientific validity, clinical utility and potential future implications of such services are being hotly debated, several ethical and regulatory questions related to direct-to-consumer (DTC) marketing strategies of genetic tests have not yet received sufficient attention. For example, how can we minimize the risk of unauthorized third parties from submitting other people's DNA for testing? Another pressing question concerns the ownership of (genotypic and phenotypic) information, as well as the unclear legal status of customers regarding their own personal information. Current legislation in the US and Europe falls short of providing clear answers to these questions. Until the regulation of personal genomics services catches up with the technology, we call upon commercial providers to self-regulate and coordinate their activities to minimize potential risks to individual privacy. We also point out some specific steps, along the trustee model, that providers of DTC personal genomics services as well as regulators and policy makers could consider for addressing some of the concerns raised below.

  6. Nutritional genomics.

    Science.gov (United States)

    Ordovas, Jose M; Corella, Dolores

    2004-01-01

    Nutritional genomics has tremendous potential to change the future of dietary guidelines and personal recommendations. Nutrigenetics will provide the basis for personalized dietary recommendations based on the individual's genetic make up. This approach has been used for decades for certain monogenic diseases; however, the challenge is to implement a similar concept for common multifactorial disorders and to develop tools to detect genetic predisposition and to prevent common disorders decades before their manifestation. The preliminary results involving gene-diet interactions for cardiovascular diseases and cancer are promising, but mostly inconclusive. Success in this area will require the integration of different disciplines and investigators working on large population studies designed to adequately investigate gene-environment interactions. Despite the current difficulties, preliminary evidence strongly suggests that the concept should work and that we will be able to harness the information contained in our genomes to achieve successful aging using behavioral changes; nutrition will be the cornerstone of this endeavor.

  7. Visualization for genomics: the Microbial Genome Viewer.

    NARCIS (Netherlands)

    Kerkhoven, R.; Enckevort, F.H.J. van; Boekhorst, J.; Molenaar, D; Siezen, R.J.

    2004-01-01

    SUMMARY: A Web-based visualization tool, the Microbial Genome Viewer, is presented that allows the user to combine complex genomic data in a highly interactive way. This Web tool enables the interactive generation of chromosome wheels and linear genome maps from genome annotation data stored in a

  8. Anterior referencing of tibial slope in total knee arthroplasty considerably influences knee kinematics: a musculoskeletal simulation study.

    Science.gov (United States)

    Marra, Marco A; Strzelczak, Marta; Heesterbeek, Petra J C; van de Groes, Sebastiaan A W; Janssen, Dennis W; Koopman, Bart F J M; Wymenga, Ate B; Verdonschot, Nico J J

    2017-05-12

    In total knee arthroplasty (TKA), the posterior tibial slope is not always reconstructed correctly, and the knee ligaments may become too tight in flexion. To release a tight flexion gap, surgeons can increase the posterior tibial slope using two surgical resection techniques: the anterior tibial cortex (ACR) or the centre of tibial plateau (CPR) referencing. It is not known how this choice affects the knee laxity and function during activities of daily living. The aim of this study was to investigate the effect of tibial slope on knee laxity, kinematics and forces during a squatting activity using computer simulation techniques. We hypothesised that the effects depend on the referencing technique utilised. A validated musculoskeletal model of TKA was used. Knee laxity tests were simulated in flexion and extension. Then, a squat motion was simulated to calculate: movement of the tibiofemoral joint (TFJ) contact points and patello-femoral joint (PFJ) contact force. All analyses were repeated with more anterior (-3°), neutral (0°), and more posterior tibial slope (+3°, +6°, +9°), and with two referencing techniques (ACR, CPR). Knee laxities increased dramatically with more posterior slope with the ACR technique (up to 400%), both in flexion and in extension. The CPR technique, instead, had much smaller effects (up to 42% variations). During squatting, more slope with the ACR technique resulted in larger movements of the TFJ contact point. The PFJ contact force decreased considerably with more slope with the CPR technique (12% body weight reduction every 3° more posterior slope), thanks to the preservation of the patellar height and quadriceps-femur load sharing. ACR technique alters considerably the knee laxity, both in flexion and extensions, and surgeons should be cautious about its use. More slope with CPR technique induces more favourable TFJ kinematics and loading of the knee extensor apparatus and does not substantially alter knee laxity. Preferably, the

  9. Amperometric Detection of Sub-ppm Formaldehyde Using Single-Walled Carbon Nanotubes and Hydroxylamines: A Referenced Chemiresistive System.

    Science.gov (United States)

    Ishihara, Shinsuke; Labuta, Jan; Nakanishi, Takashi; Tanaka, Takeshi; Kataura, Hiromichi

    2017-10-27

    We report amperometric detection of formaldehyde (HCHO) using hydroxylamine hydrochloride and single-walled carbon nanotubes (SWCNTs). Hydroxylamine hydrochloride reacts with HCHO to emit HCl vapor, which injects a hole carrier into semiconducting SWCNTs. The increase of conductivity in SWCNTs is easily monitored using an ohmmeter. The debundling of SWCNTs with a metallo-supramolecular polymer (MSP) increased the active surface area in the SWCNTs network, leading to excellent sensitivity to HCHO with a limit of detection (LoD) of 0.016 ppm. The response of sensor is reversible, and the sensor is reusable. The selectivity to HCHO is 10 5 -10 6 times higher than interferences with other volatiles such as water, methanol, and toluene. Moreover, false-positive responses caused by a significant variation of humidity and/or temperature are successfully discriminated from true-positive responses by using two sensors, one with and the other without hydroxylamine hydrochloride, in a referenced system.

  10. Ultrahigh Dimensional Variable Selection for Interpolation of Point Referenced Spatial Data: A Digital Soil Mapping Case Study.

    Science.gov (United States)

    Fitzpatrick, Benjamin R; Lamb, David W; Mengersen, Kerrie

    2016-01-01

    Modern soil mapping is characterised by the need to interpolate point referenced (geostatistical) observations and the availability of large numbers of environmental characteristics for consideration as covariates to aid this interpolation. Modelling tasks of this nature also occur in other fields such as biogeography and environmental science. This analysis employs the Least Angle Regression (LAR) algorithm for fitting Least Absolute Shrinkage and Selection Operator (LASSO) penalized Multiple Linear Regressions models. This analysis demonstrates the efficiency of the LAR algorithm at selecting covariates to aid the interpolation of geostatistical soil carbon observations. Where an exhaustive search of the models that could be constructed from 800 potential covariate terms and 60 observations would be prohibitively demanding, LASSO variable selection is accomplished with trivial computational investment.

  11. The design of a mechanical referencing system for the rear drum of the Longwall Shearer Coal Miner

    Science.gov (United States)

    Jones, E. W.; Yang, T. C. H.

    1981-01-01

    The design of two systems which reference the position of a longwall shearer coal miner to the mine roof of the present cut and of the last cut are presented. This system is part of an automation system that will guide the rear cutting drum in such a manner that the total depth of cut remains constant even though the front drum may be following an undulating roof profile. The rear drum referencing mechanism continually monitors the distance from the mine roof to the floor for the present cut. This system provides a signal to control a constant depth of cut. The last cut follower mechanism continually monitors the distance from the mine roof of the prior cut to the cutting drum. This latter system provides a signal to minimize the step height in the roof between cuts. The dynamic response of this hydraulic-pneumatic and mechanical system is analyzed to determine accumulator size and precharge pressure.

  12. Attribution, referencing and commencing HE students as novice academic writers: Giving them more time to ‘get it’

    Directory of Open Access Journals (Sweden)

    John Hamilton

    2016-07-01

    Full Text Available The requirement for commencing higher education students to apply principles of attribution in their early academic writing frequently creates frustration both for students and academic teaching staff. Teachers often provide information on the necessity of attribution, and considerable detail on the mechanics of how to reference, and express frustration at the failure of some students to demonstrate this in their writing. In turn, many students appear overwhelmed and confused by the expectations placed on them as early academic writers. This paper explores these expectations and questions current assessment practices, advocating a longer period of formative learning before students are required to competently and accurately apply attribution principles and referencing conventions in their writing. Using the threshold concept framework (Meyer & Land, 2005, it suggests viewing attribution as a ‘conceptual gateway’ through which students must pass in becoming academic writers, and explores some implications of this for teaching, learning and assessment.

  13. Improved phase sensitivity in spectral domain phase microscopy using line-field illumination and self phase-referencing

    Science.gov (United States)

    Yaqoob, Zahid; Choi, Wonshik; Oh, Seungeun; Lue, Niyom; Park, Yongkeun; Fang-Yen, Christopher; Dasari, Ramachandra R.; Badizadegan, Kamran; Feld, Michael S.

    2010-01-01

    We report a quantitative phase microscope based on spectral domain optical coherence tomography and line-field illumination. The line illumination allows self phase-referencing method to reject common-mode phase noise. The quantitative phase microscope also features a separate reference arm, permitting the use of high numerical aperture (NA > 1) microscope objectives for high resolution phase measurement at multiple points along the line of illumination. We demonstrate that the path-length sensitivity of the instrument can be as good as 41 pm/Hz, which makes it suitable for nanometer scale study of cell motility. We present the detection of natural motions of cell surface and two-dimensional surface profiling of a HeLa cell. PMID:19550464

  14. Ultrahigh Dimensional Variable Selection for Interpolation of Point Referenced Spatial Data: A Digital Soil Mapping Case Study

    Science.gov (United States)

    Lamb, David W.; Mengersen, Kerrie

    2016-01-01

    Modern soil mapping is characterised by the need to interpolate point referenced (geostatistical) observations and the availability of large numbers of environmental characteristics for consideration as covariates to aid this interpolation. Modelling tasks of this nature also occur in other fields such as biogeography and environmental science. This analysis employs the Least Angle Regression (LAR) algorithm for fitting Least Absolute Shrinkage and Selection Operator (LASSO) penalized Multiple Linear Regressions models. This analysis demonstrates the efficiency of the LAR algorithm at selecting covariates to aid the interpolation of geostatistical soil carbon observations. Where an exhaustive search of the models that could be constructed from 800 potential covariate terms and 60 observations would be prohibitively demanding, LASSO variable selection is accomplished with trivial computational investment. PMID:27603135

  15. Redefining the Practice of Peer Review Through Intelligent Automation Part 1: Creation of a Standardized Methodology and Referenceable Database.

    Science.gov (United States)

    Reiner, Bruce I

    2017-10-01

    Conventional peer review practice is compromised by a number of well-documented biases, which in turn limit standard of care analysis, which is fundamental to determination of medical malpractice. In addition to these intrinsic biases, other existing deficiencies exist in current peer review including the lack of standardization, objectivity, retrospective practice, and automation. An alternative model to address these deficiencies would be one which is completely blinded to the peer reviewer, requires independent reporting from both parties, utilizes automated data mining techniques for neutral and objective report analysis, and provides data reconciliation for resolution of finding-specific report differences. If properly implemented, this peer review model could result in creation of a standardized referenceable peer review database which could further assist in customizable education, technology refinement, and implementation of real-time context and user-specific decision support.

  16. DactyLoc : A minimally geo-referenced WiFi+GSM-fingerprint-based localization method for positioning in urban spaces

    DEFF Research Database (Denmark)

    Cujia, Kristian; Wirz, Martin; Kjærgaard, Mikkel Baun

    2012-01-01

    Fingerprinting-based localization methods relying on WiFi and GSM information provide sufficient localization accuracy for many mobile phone applications. Most of the existing approaches require a training set consisting of geo-referenced fingerprints to build a reference database. We propose...... a collaborative, semi-supervised WiFi+GSM fingerprinting method where only a small fraction of all fingerprints needs to be geo-referenced. Our approach enables indexing of areas in the absence of GPS reception as often found in urban spaces and indoors without manual labeling of fingerprints. The method takes...

  17. A self-referencing biosensor for real-time monitoring of physiological ATP transport in plant systems.

    Science.gov (United States)

    Vanegas, Diana C; Clark, Greg; Cannon, Ashley E; Roux, Stanley; Chaturvedi, Prachee; McLamore, Eric S

    2015-12-15

    The objective of this study was to develop a self-referencing electrochemical biosensor for the direct measurement of ATP flux into the extracellular matrix by living cells/organisms. The working mechanism of the developed biosensor is based on the activity of glycerol kinase and glycerol-3-phosphate oxidase. A stratified bi-enzyme nanocomposite was created using a protein-templated silica sol gel encapsulation technique on top of graphene-modified platinum electrodes. The biosensor exhibited excellent electrochemical performance with a sensitivity of 2.4±1.8 nA/µM, a response time of 20±13 s and a lower detection limit of 1.3±0.7 nM. The self-referencing biosensor was used to measure exogenous ATP efflux by (i) germinating Ceratopteris spores and (ii) growing Zea mays L. roots. This manuscript demonstrates the first development of a non-invasive ATP micro-biosensor for the direct measurement of eATP transport in living tissues. Before this work, assays of eATP have not been able to record the temporally transient movement of ATP at physiological levels (nM and sub-nM). The method demonstrated here accurately measured [eATP] flux in the immediate vicinity of plant cells. Although these proof of concept experiments focus on plant tissues, the technique developed herein is applicable to any living tissue, where nanomolar concentrations of ATP play a critical role in signaling and development. This tool will be invaluable for conducting hypothesis-driven life science research aimed at understanding the role of ATP in the extracellular environment. Copyright © 2015 Elsevier B.V. All rights reserved.

  18. Geospatial cryptography: enabling researchers to access private, spatially referenced, human subjects data for cancer control and prevention.

    Science.gov (United States)

    Jacquez, Geoffrey M; Essex, Aleksander; Curtis, Andrew; Kohler, Betsy; Sherman, Recinda; Emam, Khaled El; Shi, Chen; Kaufmann, Andy; Beale, Linda; Cusick, Thomas; Goldberg, Daniel; Goovaerts, Pierre

    2017-07-01

    As the volume, accuracy and precision of digital geographic information have increased, concerns regarding individual privacy and confidentiality have come to the forefront. Not only do these challenge a basic tenet underlying the advancement of science by posing substantial obstacles to the sharing of data to validate research results, but they are obstacles to conducting certain research projects in the first place. Geospatial cryptography involves the specification, design, implementation and application of cryptographic techniques to address privacy, confidentiality and security concerns for geographically referenced data. This article defines geospatial cryptography and demonstrates its application in cancer control and surveillance. Four use cases are considered: (1) national-level de-duplication among state or province-based cancer registries; (2) sharing of confidential data across cancer registries to support case aggregation across administrative geographies; (3) secure data linkage; and (4) cancer cluster investigation and surveillance. A secure multi-party system for geospatial cryptography is developed. Solutions under geospatial cryptography are presented and computation time is calculated. As services provided by cancer registries to the research community, de-duplication, case aggregation across administrative geographies and secure data linkage are often time-consuming and in some instances precluded by confidentiality and security concerns. Geospatial cryptography provides secure solutions that hold significant promise for addressing these concerns and for accelerating the pace of research with human subjects data residing in our nation's cancer registries. Pursuit of the research directions posed herein conceivably would lead to a geospatially encrypted geographic information system (GEGIS) designed specifically to promote the sharing and spatial analysis of confidential data. Geospatial cryptography holds substantial promise for accelerating the

  19. Spatial analysis and mapping of malaria risk in Malawi using point-referenced prevalence of infection data

    Directory of Open Access Journals (Sweden)

    Kazembe Lawrence N

    2006-09-01

    Full Text Available Abstract Background Current malaria control initiatives aim at reducing malaria burden by half by the year 2010. Effective control requires evidence-based utilisation of resources. Characterizing spatial patterns of risk, through maps, is an important tool to guide control programmes. To this end an analysis was carried out to predict and map malaria risk in Malawi using empirical data with the aim of identifying areas where greatest effort should be focussed. Methods Point-referenced prevalence of infection data for children aged 1–10 years were collected from published and grey literature and geo-referenced. The model-based geostatistical methods were applied to analyze and predict malaria risk in areas where data were not observed. Topographical and climatic covariates were added in the model for risk assessment and improved prediction. A Bayesian approach was used for model fitting and prediction. Results Bivariate models showed a significant association of malaria risk with elevation, annual maximum temperature, rainfall and potential evapotranspiration (PET. However in the prediction model, the spatial distribution of malaria risk was associated with elevation, and marginally with maximum temperature and PET. The resulting map broadly agreed with expert opinion about the variation of risk in the country, and further showed marked variation even at local level. High risk areas were in the low-lying lake shore regions, while low risk was along the highlands in the country. Conclusion The map provided an initial description of the geographic variation of malaria risk in Malawi, and might help in the choice and design of interventions, which is crucial for reducing the burden of malaria in Malawi.

  20. Genome Sequencing

    DEFF Research Database (Denmark)

    Sato, Shusei; Andersen, Stig Uggerhøj

    2014-01-01

    The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based...... on transcriptional evidence. Analysis of repetitive sequences suggests that they are underrepresented in the reference assembly, reflecting an enrichment of gene-rich regions in the current assembly. Characterization of Lotus natural variation by resequencing of L. japonicus accessions and diploid Lotus species...... is currently ongoing, facilitated by the MG20 reference sequence...

  1. The platypus genome unraveled.

    Science.gov (United States)

    O'Brien, Stephen J

    2008-06-13

    The genome of the platypus has been sequenced, assembled, and annotated by an international genomics team. Like the animal itself the platypus genome contains an amalgam of mammal, reptile, and bird-like features.

  2. Publically accessible decision support system of the spatially referenced regressions on watershed attributes (SPARROW) model and model enhancements in South Carolina

    Science.gov (United States)

    Celeste Journey; Anne B. Hoos; David E. Ladd; John W. brakebill; Richard A. Smith

    2016-01-01

    The U.S. Geological Survey (USGS) National Water Quality Assessment program has developed a web-based decision support system (DSS) to provide free public access to the steady-stateSPAtially Referenced Regressions On Watershed attributes (SPARROW) model simulation results on nutrient conditions in streams and rivers and to offer scenario testing capabilities for...

  3. Indirect-Collective Referencing (ICR) in the Elite Journal Literature of Physics. I.A Literature Science Study on the Journal Level.

    Science.gov (United States)

    Szava-Kovats, Endre

    2001-01-01

    Reports findings of an Indirect-Collective Referencing (ICR) investigation carried out in a representative sample of the elite physics journal literature, "The Physical Review," in the January 1997 issues of 44 source journals. Findings revealed ICR phenomenon present in all journals, that the quantity of non-indexed ICRs in this literature…

  4. 40 CFR Appendix I to Subpart A of... - Global Warming Potentials (Mass Basis), Referenced to the Absolute GWP for the Adopted Carbon...

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 17 2010-07-01 2010-07-01 false Global Warming Potentials (Mass Basis..., App. I Appendix I to Subpart A of Part 82—Global Warming Potentials (Mass Basis), Referenced to the... formula Global warming potential (time horizon) 20 years 100 years 500 years CFC-11 CFCl3 5000 4000 1400...

  5. Spatially Referenced Educational Achievement Data Exploration: A Web-Based Interactive System Integration of GIS, PHP, and MySQL Technologies

    Science.gov (United States)

    Mulvenon, Sean W.; Wang, Kening; Mckenzie, Sarah; Anderson, Travis

    2006-01-01

    Effective exploration of spatially referenced educational achievement data can help educational researchers and policy analysts speed up gaining valuable insight into datasets. This article illustrates a demo system developed in the National Office for Research on Measurement and Evaluation Systems (NORMES) for supporting Web-based interactive…

  6. Cohesive Referencing Errors During Narrative Production as Clinical Evidence of Central Nervous System Abnormality in School-Aged Children With Fetal Alcohol Spectrum Disorders.

    Science.gov (United States)

    Thorne, John C; Coggins, Truman E

    2016-11-01

    Previous evidence suggests that cohesive referencing errors made during narratives may be a behavior that is revealing of underlying central nervous system abnormality in children with fetal alcohol spectrum disorders (FASD). The current research extends this evidence. Retrospective analysis of narrative and clinical data from 152 children (ages 6 to 14), 72 of whom had confirmed FASD, was used. Narrative analysis was conducted blind to diagnostic status, age, or gender. Group performance was compared. The associations between measures of cohesive referencing and clinically gathered indices of the degree of central nervous system abnormality were examined. Results show clear associations between elevated rates of cohesive referencing errors and central nervous system abnormality. Elevated error rates were more common in children with FASD than those without, and prevalence increased predictably across groups with more severe central nervous system abnormality. Risk is particularly elevated for those with microcephaly or a diagnosis of fetal alcohol syndrome. Cohesive referencing errors during narrative are a viable behavioral marker of the kinds of central nervous system abnormality associated with prenatal alcohol exposure, having significant potential to become a valuable diagnostic and research tool.

  7. 29 CFR Appendix B to Subpart B of... - Reprint of U.S. Coast Guard Regulations Referenced in Subpart B, for Determination of Coast Guard...

    Science.gov (United States)

    2010-07-01

    ... Subpart B, for Determination of Coast Guard Authorized Persons B Appendix B to Subpart B of Part 1915... Enclosed Spaces and Other Dangerous Atmospheres in Shipyard Employment Pt. 1915, Subpt. B, App. B Appendix B to Subpart B of Part 1915—Reprint of U.S. Coast Guard Regulations Referenced in Subpart B, for...

  8. Narrator Point of View and Persuasion in Health Narratives: The Role of Protagonist-Reader Similarity, Identification, and Self-Referencing.

    Science.gov (United States)

    Chen, Meng; Bell, Robert A; Taylor, Laramie D

    2016-08-01

    Narratives are often used in messages about health threats. We posited that a 1st-person point of view (POV) narrative would have a greater effect than a 3rd-person POV on the mediators identification and self-referencing-an effect moderated by protagonist-reader similarity. Higher levels of identification and self-referencing were expected to elevate susceptibility and severity perceptions, leading to persuasion. Participants ages ≤30 years were recruited from a crowdsource website and randomly assigned to read one version of a faux magazine article about caffeine overdose. Article versions were defined by a 2 (1st- or 3rd-person POV) × 2 (similar or dissimilar protagonist) design. To manipulate similarity, we had respondents read an article in which the protagonist was also young (24 years of age) and of the same sex or much older (54 years of age) and of the opposite sex. Participants then completed a questionnaire measuring study variables. Contrary to expectations, POV did not affect identification or self-referencing. However, similarity directly impacted identification, which in turn influenced severity perceptions. Self-referencing was not affected by the experimental manipulations but had a direct effect on susceptibility and also mediated the identification → susceptibility relationship. Susceptibility and severity perceptions were associated with greater levels of persuasion. Implications for message design are discussed.

  9. Genome cartography: charting the apicomplexan genome.

    Science.gov (United States)

    Kissinger, Jessica C; DeBarry, Jeremy

    2011-08-01

    Genes reside in particular genomic contexts that can be mapped at many levels. Historically, 'genetic maps' were used primarily to locate genes. Recent technological advances in the determination of genome sequences have made the analysis and comparison of whole genomes possible and increasingly tractable. What do we see if we shift our focus from gene content (the 'inventory' of genes contained within a genome) to the composition and organization of a genome? This review examines what has been learned about the evolution of the apicomplexan genome as well as the significance and impact of genomic location on our understanding of the eukaryotic genome and parasite biology. Copyright © 2011 Elsevier Ltd. All rights reserved.

  10. Herbarium genomics

    DEFF Research Database (Denmark)

    Bakker, Freek T.; Lei, Di; Yu, Jiaying

    2016-01-01

    Herbarium genomics is proving promising as next-generation sequencing approaches are well suited to deal with the usually fragmented nature of archival DNA. We show that routine assembly of partial plastome sequences from herbarium specimens is feasible, from total DNA extracts and with specimens...... Angiosperm families, 73 of which were from herbarium material with ages up to 146 years old. For 84 specimens, a sufficient number of paired-end reads were generated (in total 9.4 × 1012 nucleotides), yielding successful plastome assemblies for 74 specimens. Those derived from herbarium specimens have lower...... fractions of plastome-derived reads compared with those from fresh and silica-gel-dried specimens, but total herbarium assembly lengths are only slightly shorter. Specimens from wet-tropical conditions appear to have a higher number of contigs per assembly and lower N50 values. We find no significant...

  11. National Human Genome Research Institute

    Science.gov (United States)

    ... the Director Organization Reports & Publications Español The National Human Genome Research Institute conducts genetic and genomic research, funds ... genomic literacy among physicians. Funded by the National Human Genome Research Institute (NHGRI), The Universal Genomics Instructor Handbook ...

  12. Complete Chloroplast Genome of Tanaecium tetragonolobum: The First Bignoniaceae Plastome.

    Directory of Open Access Journals (Sweden)

    Alison Gonçalves Nazareno

    Full Text Available Bignoniaceae is a Pantropical plant family that is especially abundant in the Neotropics. Members of the Bignoniaceae are diverse in many ecosystems and represent key components of the Tropical flora. Despite the ecological importance of the Bignoniaceae and all the efforts to reconstruct the phylogeny of this group, whole chloroplast genome information has not yet been reported for any members of the family. Here, we report the complete chloroplast genome sequence of Tanaecium tetragonolobum (Jacq. L.G. Lohmann, which was reconstructed using de novo and referenced-based assembly of single-end reads generated by shotgun sequencing of total genomic DNA in an Illumina platform. The gene order and organization of the chloroplast genome of T. tetragonolobum exhibits the general structure of flowering plants, and is similar to other Lamiales chloroplast genomes. The chloroplast genome of T. tetragonolobum is a circular molecule of 153,776 base pairs (bp with a quadripartite structure containing two single copy regions, a large single copy region (LSC, 84,612 bp and a small single copy region (SSC, 17,586 bp separated by inverted repeat regions (IRs, 25,789 bp. In addition, the chloroplast genome of T. tetragonolobum has 38.3% GC content and includes 121 genes, of which 86 are protein-coding, 31 are transfer RNA, and four are ribosomal RNA. The chloroplast genome of T. tetragonolobum presents a total of 47 tandem repeats and 347 simple sequence repeats (SSRs with mononucleotides being the most common and di-, tri-, tetra-, and hexanucleotides occurring with less frequency. The results obtained here were compared to other chloroplast genomes of Lamiales available to date, providing new insight into the evolution of chloroplast genomes within Lamiales. Overall, the evolutionary rates of genes in Lamiales are lineage-, locus-, and region-specific, indicating that the evolutionary pattern of nucleotide substitution in chloroplast genomes of flowering

  13. Effects of Body Orientation and Retinal Image Pitch on the Perception of Gravity-Referenced Eye Level (GREL)

    Science.gov (United States)

    Cohen, Malcolm M.; Guzy, Larry T.; Wade, Charles E. (Technical Monitor)

    1994-01-01

    It has been asserted that the pitch orientation of a visual array and of an observer's body jointly determine the perception of GREL. The current study formally tests this assertion over an extended range with multiple combinations of visual and body pitch orientations. Ten subjects were individually secured in a Circolectric bed surrounded by a room (pitchroom) with walls that could be pitched at various angles with respect to gravity. The bed and the walls of the room were independently adjusted to each of five positions relative to gravitational vertical: -15, -7.5, 0, +7.5, and +15 degrees, yielding 25 combinations of body x room pitch angles, and retinal image pitch (RIP) conditions ranging from -30 to +30 degrees. Each subject set a target to apparent GREL while viewing it against a background of two electroluminescent strips on the outer edges of the far wall of the room. As determined by ANOVA, the orientation of the room, and its interaction with that of the observer, significantly altered GREL (p less than 0.01). Regression analysis showed that GREL was best described as a linear summation of the weighted independent contributions from a body-referenced mechanism (B) and a visual mechanism given by the orientation of the background array on the retina (RIP). The equation for this relationship is: GREL = .74 (B) +.64 (RIP) - 1.42; r-squared = .994.

  14. Sub-Doppler Resolution Spectroscopy of the Fundamental Vibration Band of HCl with a Comb-Referenced Spectrometer

    Science.gov (United States)

    Iwakuni, Kana; Sera, Hideyuki; Abe, Masashi; Sasada, Hiroyuki

    2015-06-01

    Sub-Doppler resolution spectroscopy of the fundamental bands of H35Cl and H37Cl has been carried out from 87 to 90 THz using a comb-referenced difference-frequency-generation (DFG) spectrometer. While the frequencies of the pump and signal waves are locked to that of the individual nearest comb mode, the repetition rate of the comb is varied for sweeping the idler frequency. Therefore, the relative uncertainty of the frequency scale is 10-11, and the spectral resolution remains about 250 kHz even when the spectrum is accumulated for a long time. The hyperfine structures caused by chlorine nucleus are resolved for the R(0) to R(4) transitions. The figure depicts wavelength-modulation spectrum of the R(0) transition of H35Cl. Three Lamb dips correspond to the F= 0, 1, and -1 components left to right, and the others with arrows are cross-over resonances which are useful for determining the weak F=-1 component frequencies for the R(1) to R(3) transitions. We have determined 49 and 44 transition frequencies of H35Cl and H37Cl with an uncertainty of 10 kHz. Six molecular constants of the vibrational excited state for each isotopomer are determined. They reproduce the determined frequencies with a standard deviation of about 10 kHz.

  15. The grain of spatially referenced economic cost and biodiversity benefit data and the effectiveness of a cost targeting strategy.

    Science.gov (United States)

    Sutton, N J; Armsworth, P R

    2014-12-01

    Facing tight resource constraints, conservation organizations must allocate funds available for habitat protection as effectively as possible. Often, they combine spatially referenced economic and biodiversity data to prioritize land for protection. We tested how sensitive these prioritizations could be to differences in the spatial grain of these data by demonstrating how the conclusion of a classic debate in conservation planning between cost and benefit targeting was altered based on the available information. As a case study, we determined parcel-level acquisition costs and biodiversity benefits of land transactions recently undertaken by a nonprofit conservation organization that seeks to protect forests in the eastern United States. Then, we used hypothetical conservation plans to simulate the types of ex ante priorities that an organization could use to prioritize areas for protection. We found the apparent effectiveness of cost and benefit targeting depended on the spatial grain of the data used when prioritizing parcels based on local species richness. However, when accounting for complementarity, benefit targeting consistently was more efficient than a cost targeting strategy regardless of the spatial grain of the data involved. More pertinently for other studies, we found that combining data collected over different spatial grains inflated the apparent effectiveness of a cost targeting strategy and led to overestimation of the efficiency gain offered by adopting a more integrative return-on-investment approach. © 2014 Society for Conservation Biology.

  16. Referencing techniques for high-speed confocal fluorescence lifetime imaging microscopy (FLIM) based on analog mean-delay (AMD) method

    Science.gov (United States)

    Kim, Byungyeon; Lee, Minsuk; Park, Byungjun; Lee, Seungrag; Won, Youngjae

    2017-02-01

    Analog mean-delay (AMD) method is a new powerful alternative method in determining the lifetime of a fluorescence molecule for high-speed confocal fluorescence lifetime imaging microscopy (FLIM). Even though the photon economy and the lifetime precision of the AMD method are proven to be as good as the state-of-the-art time-correlated single photon counting (TC-SPC) method, there have been some speculations and concerns about the accuracy of this method. In the AMD method, the temporal waveform of an emitted fluorescence signal is directly recorded with a slow digitizer whose bandwidth is much lower than the temporal resolution of lifetime to be measured. We found that the drifts and the fluctuations of the absolute zero position in a measured temporal waveform are the major problems in the AMD method. As a referencing technique, we already proposed dual-channel waveform measurement scheme that may suppress these errors. In this study, we have demonstrated real-time confocal AMD-FLIM system with dual-channel waveform measurement technique.

  17. The use of low resistivity substrates for optimal noise reduction, ground referencing, and current conduction in mixed signal ASICs

    Energy Technology Data Exchange (ETDEWEB)

    Zimmerman, T.

    1997-12-01

    This paper is distilled from a talk given at the 3rd International Meeting on Front End Electronics in Taos, N.M. on Nov. 7,1997. It is based on experience gained by designing and testing the SVX3 128 channel silicon strip detector readout chip. The SVX3 chip organization is shown in Fig. 1. The Front End section consists of an integrator and analog pipeline designed at Fermilab, and the Back End section is an ADC plus sparsification and readout logic designed at LBL. SVX3 is a deadtimeless readout chip, which means that the front end is acquiring low level analog signals while the back end is digitizing and reading out digital signals. It is thus a true mixed signal chip, and demands close attention to avoid disastrous coupling from the digital to the analog sections. SVX3 is designed in a bulk CMOS process (i.e., the circuits sit in a silicon substrate). In such a process, the substrate becomes a potential coupling path. This paper discusses the effect of the substrate resistivity on coupling, and also goes into a more general discussion of grounding and referencing in mixed signal designs and how low resistivity substrates can be used to advantage. Finally, an alternative power supply current conduction method for ASICs is presented as an additional advantage which can be obtained with low resistivity substrates. 1 ref., 13 figs., 1 tab.

  18. Self-referencing Mach-Zehnder interferometer as a laser system diagnostic: Active and adaptive optical systems

    International Nuclear Information System (INIS)

    Feldman, M.; Mockler, D.J.; English, R.E. Jr.; Byrd, J.L.; Salmon, J.T.

    1991-01-01

    We are incorporating a novel self-referencing Mach-Zehnder interferometer into a large scale laser system as a real time, interactive diagnostic tool for wavefront measurement. The instrument is capable of absolute wavefront measurements accurate to better than λ/10 pv over a wavelength range > 300 nm without readjustment of the optical components. This performance is achieved through the design of both refractive optics and catadioptric collimator to achromatize the Mach-Zehnder reference arm. Other features include polarization insensitivity through the use of low angles of incidence on all beamsplitters as well as an equal path length configuration that allows measurement of either broad-band or closely spaced laser-line sources. Instrument accuracy is periodically monitored in place by means of a thermally and mechanically stable wavefront reference source that is calibrated off-line with a phase conjugate interferometer. Video interferograms are analyzed using Fourier transform techniques on a computer that includes dedicated array processor. Computer and video networks maintain distributed interferometers under the control of a single analysis computer with multiple user access. 7 refs., 11 figs

  19. The kangaroo genome

    Science.gov (United States)

    Wakefield, Matthew J.; Graves, Jennifer A. Marshall

    2003-01-01

    The kangaroo genome is a rich and unique resource for comparative genomics. Marsupial genetics and cytology have made significant contributions to the understanding of gene function and evolution, and increasing the availability of kangaroo DNA sequence information would provide these benefits on a genomic scale. Here we summarize the contributions from cytogenetic and genetic studies of marsupials, describe the genomic resources currently available and those being developed, and explore the benefits of a kangaroo genome project. PMID:12612602

  20. Genomics With Cloud Computing

    OpenAIRE

    Sukhamrit Kaur; Sandeep Kaur

    2015-01-01

    Abstract Genomics is study of genome which provides large amount of data for which large storage and computation power is needed. These issues are solved by cloud computing that provides various cloud platforms for genomics. These platforms provides many services to user like easy access to data easy sharing and transfer providing storage in hundreds of terabytes more computational power. Some cloud platforms are Google genomics DNAnexus and Globus genomics. Various features of cloud computin...

  1. Genome Maps, a new generation genome browser

    Science.gov (United States)

    Medina, Ignacio; Salavert, Francisco; Sanchez, Rubén; de Maria, Alejandro; Alonso, Roberto; Escobar, Pablo; Bleda, Marta; Dopazo, Joaquín

    2013-01-01

    Genome browsers have gained importance as more genomes and related genomic information become available. However, the increase of information brought about by new generation sequencing technologies is, at the same time, causing a subtle but continuous decrease in the efficiency of conventional genome browsers. Here, we present Genome Maps, a genome browser that implements an innovative model of data transfer and management. The program uses highly efficient technologies from the new HTML5 standard, such as scalable vector graphics, that optimize workloads at both server and client sides and ensure future scalability. Thus, data management and representation are entirely carried out by the browser, without the need of any Java Applet, Flash or other plug-in technology installation. Relevant biological data on genes, transcripts, exons, regulatory features, single-nucleotide polymorphisms, karyotype and so forth, are imported from web services and are available as tracks. In addition, several DAS servers are already included in Genome Maps. As a novelty, this web-based genome browser allows the local upload of huge genomic data files (e.g. VCF or BAM) that can be dynamically visualized in real time at the client side, thus facilitating the management of medical data affected by privacy restrictions. Finally, Genome Maps can easily be integrated in any web application by including only a few lines of code. Genome Maps is an open source collaborative initiative available in the GitHub repository (https://github.com/compbio-bigdata-viz/genome-maps). Genome Maps is available at: http://www.genomemaps.org. PMID:23748955

  2. Genome Maps, a new generation genome browser.

    Science.gov (United States)

    Medina, Ignacio; Salavert, Francisco; Sanchez, Rubén; de Maria, Alejandro; Alonso, Roberto; Escobar, Pablo; Bleda, Marta; Dopazo, Joaquín

    2013-07-01

    Genome browsers have gained importance as more genomes and related genomic information become available. However, the increase of information brought about by new generation sequencing technologies is, at the same time, causing a subtle but continuous decrease in the efficiency of conventional genome browsers. Here, we present Genome Maps, a genome browser that implements an innovative model of data transfer and management. The program uses highly efficient technologies from the new HTML5 standard, such as scalable vector graphics, that optimize workloads at both server and client sides and ensure future scalability. Thus, data management and representation are entirely carried out by the browser, without the need of any Java Applet, Flash or other plug-in technology installation. Relevant biological data on genes, transcripts, exons, regulatory features, single-nucleotide polymorphisms, karyotype and so forth, are imported from web services and are available as tracks. In addition, several DAS servers are already included in Genome Maps. As a novelty, this web-based genome browser allows the local upload of huge genomic data files (e.g. VCF or BAM) that can be dynamically visualized in real time at the client side, thus facilitating the management of medical data affected by privacy restrictions. Finally, Genome Maps can easily be integrated in any web application by including only a few lines of code. Genome Maps is an open source collaborative initiative available in the GitHub repository (https://github.com/compbio-bigdata-viz/genome-maps). Genome Maps is available at: http://www.genomemaps.org.

  3. Laying the Foundation for a Genomic Rosetta Stone: Creating Information Hubs through the User of Consensus Idenifiers

    Energy Technology Data Exchange (ETDEWEB)

    Van Brabant, Bart; Kyrpides, Nikos; Glockner, Frank Oliver; Gray, Tanya; Field, Dawn; De Vos, Paul; De Baets, Bernard; Dawyndt, Peter

    2007-05-01

    This paper presents a holistic approach that illustrates how the semantic hurdle for integration of biological databases might be overcome when mapping sources that provide information on individual genes and complete genomes to sources that provide information on the biological resources from which these sequences where derived, and vice versa. In particular we will explain how each of the completed and ongoing whole-genome sequencing projects in the Genomes OnLine Database and each of the ribosomal RNA sequences in the SILVA ribosomal RNA database have been persistently cross-referenced with the StrainInfo.net bioportal, serving both a genome centric and an organism centric view to the life on our blue planet as one more stepping stone towards the establishment of fully integrated and flexible biological information networks.

  4. An Ontology-Based GIS for Genomic Data Management of Rumen Microbes

    Directory of Open Access Journals (Sweden)

    Saber Jelokhani-Niaraki

    2015-03-01

    Full Text Available During recent years, there has been exponential growth in biological information. With the emergence of large datasets in biology, life scientists are encountering bottlenecks in handling the biological data. This study presents an integrated geographic information system (GIS-ontology application for handling microbial genome data. The application uses a linear referencing technique as one of the GIS functionalities to represent genes as linear events on the genome layer, where users can define/change the attributes of genes in an event table and interactively see the gene events on a genome layer. Our application adopted ontology to portray and store genomic data in a semantic framework, which facilitates data-sharing among biology domains, applications, and experts. The application was developed in two steps. In the first step, the genome annotated data were prepared and stored in a MySQL database. The second step involved the connection of the database to both ArcGIS and Protégé as the GIS engine and ontology platform, respectively. We have designed this application specifically to manage the genome-annotated data of rumen microbial populations. Such a GIS-ontology application offers powerful capabilities for visualizing, managing, reusing, sharing, and querying genome-related data.

  5. An Ontology-Based GIS for Genomic Data Management of Rumen Microbes.

    Science.gov (United States)

    Jelokhani-Niaraki, Saber; Tahmoorespur, Mojtaba; Minuchehr, Zarrin; Nassiri, Mohammad Reza

    2015-03-01

    During recent years, there has been exponential growth in biological information. With the emergence of large datasets in biology, life scientists are encountering bottlenecks in handling the biological data. This study presents an integrated geographic information system (GIS)-ontology application for handling microbial genome data. The application uses a linear referencing technique as one of the GIS functionalities to represent genes as linear events on the genome layer, where users can define/change the attributes of genes in an event table and interactively see the gene events on a genome layer. Our application adopted ontology to portray and store genomic data in a semantic framework, which facilitates data-sharing among biology domains, applications, and experts. The application was developed in two steps. In the first step, the genome annotated data were prepared and stored in a MySQL database. The second step involved the connection of the database to both ArcGIS and Protégé as the GIS engine and ontology platform, respectively. We have designed this application specifically to manage the genome-annotated data of rumen microbial populations. Such a GIS-ontology application offers powerful capabilities for visualizing, managing, reusing, sharing, and querying genome-related data.

  6. An Ontology-Based GIS for Genomic Data Management of Rumen Microbes

    Science.gov (United States)

    Jelokhani-Niaraki, Saber; Minuchehr, Zarrin; Nassiri, Mohammad Reza

    2015-01-01

    During recent years, there has been exponential growth in biological information. With the emergence of large datasets in biology, life scientists are encountering bottlenecks in handling the biological data. This study presents an integrated geographic information system (GIS)-ontology application for handling microbial genome data. The application uses a linear referencing technique as one of the GIS functionalities to represent genes as linear events on the genome layer, where users can define/change the attributes of genes in an event table and interactively see the gene events on a genome layer. Our application adopted ontology to portray and store genomic data in a semantic framework, which facilitates data-sharing among biology domains, applications, and experts. The application was developed in two steps. In the first step, the genome annotated data were prepared and stored in a MySQL database. The second step involved the connection of the database to both ArcGIS and Protégé as the GIS engine and ontology platform, respectively. We have designed this application specifically to manage the genome-annotated data of rumen microbial populations. Such a GIS-ontology application offers powerful capabilities for visualizing, managing, reusing, sharing, and querying genome-related data. PMID:25873847

  7. DETERMINATION OF EXTERIOR ORIENTATION PARAMETERS THROUGH DIRECT GEO-REFERENCING IN A REAL-TIME AERIAL MONITORING SYSTEM

    Directory of Open Access Journals (Sweden)

    H. Kim

    2012-07-01

    Full Text Available Rapid responses for emergency situations such as natural disasters or accidents often require geo-spatial information describing the on-going status of the affected area. Such geo-spatial information can be promptly acquired by a manned or unmanned aerial vehicle based multi-sensor system that can monitor the emergent situations in near real-time from the air using several kinds of sensors. Thus, we are in progress of developing such a real-time aerial monitoring system (RAMS consisting of both aerial and ground segments. The aerial segment acquires the sensory data about the target areas by a low-altitude helicopter system equipped with sensors such as a digital camera and a GPS/IMU system and transmits them to the ground segment through a RF link in real-time. The ground segment, which is a deployable ground station installed on a truck, receives the sensory data and rapidly processes them to generate ortho-images, DEMs, etc. In order to generate geo-spatial information, in this system, exterior orientation parameters (EOP of the acquired images are obtained through direct geo-referencing because it is difficult to acquire coordinates of ground points in disaster area. The main process, since the data acquisition stage until the measurement of EOP, is discussed as follows. First, at the time of data acquisition, image acquisition time synchronized by GPS time is recorded as part of image file name. Second, the acquired data are then transmitted to the ground segment in real-time. Third, by processing software for ground segment, positions/attitudes of acquired images are calculated through a linear interpolation using the GPS time of the received position/attitude data and images. Finally, the EOPs of images are obtained from position/attitude data by deriving the relationships between a camera coordinate system and a GPS/IMU coordinate system. In this study, we evaluated the accuracy of the EOP decided by direct geo-referencing in our system

  8. Genomic Encyclopedia of Fungi

    Energy Technology Data Exchange (ETDEWEB)

    Grigoriev, Igor

    2012-08-10

    Genomes of fungi relevant to energy and environment are in focus of the Fungal Genomic Program at the US Department of Energy Joint Genome Institute (JGI). Its key project, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts), and explores fungal diversity by means of genome sequencing and analysis. Over 150 fungal genomes have been sequenced by JGI to date and released through MycoCosm (www.jgi.doe.gov/fungi), a fungal web-portal, which integrates sequence and functional data with genome analysis tools for user community. Sequence analysis supported by functional genomics leads to developing parts list for complex systems ranging from ecosystems of biofuel crops to biorefineries. Recent examples of such parts suggested by comparative genomics and functional analysis in these areas are presented here.

  9. JGI Fungal Genomics Program

    Energy Technology Data Exchange (ETDEWEB)

    Grigoriev, Igor V.

    2011-03-14

    Genomes of energy and environment fungi are in focus of the Fungal Genomic Program at the US Department of Energy Joint Genome Institute (JGI). Its key project, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts), and explores fungal diversity by means of genome sequencing and analysis. Over 50 fungal genomes have been sequenced by JGI to date and released through MycoCosm (www.jgi.doe.gov/fungi), a fungal web-portal, which integrates sequence and functional data with genome analysis tools for user community. Sequence analysis supported by functional genomics leads to developing parts list for complex systems ranging from ecosystems of biofuel crops to biorefineries. Recent examples of such 'parts' suggested by comparative genomics and functional analysis in these areas are presented here

  10. Dual lifetime referencing enables pH-control for oxidoreductions in hydrogel-stabilized biphasic reaction systems.

    Science.gov (United States)

    Begemann, Jens; Spiess, Antje C

    2015-09-01

    pH-shifts are a serious challenge in cofactor dependent biocatalytic oxidoreductions. Therefore, a pH control strategy was developed for reaction systems, where the pH value is not directly measurable. Such a reaction system is the biphasic aqueous-organic reaction system, where the oxidoreduction of hydrophobic substrates in organic solvents is catalysed by hydrogel-immobilized enzymes, and enzyme-coupled cofactor regeneration is accomplished via formate dehydrogenase, leading to a pH-shift. Dual lifetime referencing (DLR), a fluorescence spectroscopic method, was applied for online-monitoring of the pH-value within the immobilizates during the reaction, allowing for a controlled dosage of formic acid. It could be shown that by applying trisodium 8-hydroxypyrene-1, 3, 6-trisulfonate as pH indicator and Ru(II) tris(4, 7-diphenyl-1, 10-phenantroline) (Ru[dpp]) as a reference luminophore the control of the pH-value in a macroscopic gel-bead-stabilized aqueous/organic two phase system in a range of pH 6.5 to 8.0 is possible. An experimental proof of concept could maintain a stable pH of 7.5 ± 0.15 during the reaction for at least 105 h. With these results, it could be shown that DLR is a powerful tool for pH-control within reaction systems with no direct access for conventional pH-measurement. Copyright © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Highly sensitive detection of nanoparticles with a self-referenced and self-heterodyned whispering-gallery Raman microlaser

    Science.gov (United States)

    Özdemir, Şahin Kaya; Zhu, Jiangang; Yang, Xu; Peng, Bo; Yilmaz, Huzeyfe; He, Lina; Monifi, Faraz; Huang, Steven He; Long, Gui Lu; Yang, Lan

    2014-01-01

    Optical whispering-gallery-mode resonators (WGMRs) have emerged as promising platforms for label-free detection of nano-objects. The ultimate sensitivity of WGMRs is determined by the strength of the light–matter interaction quantified by quality factor/mode volume, Q/V, and the resolution is determined by Q. To date, to improve sensitivity and precision of detection either WGMRs have been doped with rare-earth ions to compensate losses and increase Q or plasmonic resonances have been exploited for their superior field confinement and lower V. Here, we demonstrate, for the first time to our knowledge, enhanced detection of single-nanoparticle-induced mode splitting in a silica WGMR via Raman gain-assisted loss compensation and WGM Raman microlaser. In particular, the use of the Raman microlaser provides a dopant-free, self-referenced, and self-heterodyned scheme with a detection limit ultimately determined by the thermorefractive noise. Notably, we detected and counted individual nanoparticles with polarizabilities down to 3.82 × 10−6 μm3 by monitoring a heterodyne beatnote signal. This level of sensitivity is achieved without exploiting plasmonic effects, external references, or active stabilization and frequency locking. Single nanoparticles are detected one at a time; however, their characterization by size or polarizability requires ensemble measurements and statistical averaging. This dopant-free scheme retains the inherited biocompatibility of silica and could find widespread use for sensing in biological media. The Raman laser and operation band of the sensor can be tailored for the specific sensing environment and the properties of the targeted materials by changing the pump laser wavelength. This scheme also opens the possibility of using intrinsic Raman or parametric gain for loss compensation in other systems where dissipation hinders progress and limits applications. PMID:25197086

  12. Proposed Standards for Variable Harmonization Documentation and Referencing: A Case Study Using QuickCharmStats 1.1.

    Directory of Open Access Journals (Sweden)

    Kristi Winters

    Full Text Available Comparative statistical analyses often require data harmonization, yet the social sciences do not have clear operationalization frameworks that guide and homogenize variable coding decisions across disciplines. When faced with a need to harmonize variables researchers often look for guidance from various international studies that employ output harmonization, such as the Comparative Survey of Election Studies, which offer recoding structures for the same variable (e.g. marital status. More problematically there are no agreed documentation standards or journal requirements for reporting variable harmonization to facilitate a transparent replication process. We propose a conceptual and data-driven digital solution that creates harmonization documentation standards for publication and scholarly citation: QuickCharmStats 1.1. It is free and open-source software that allows for the organizing, documenting and publishing of data harmonization projects. QuickCharmStats starts at the conceptual level and its workflow ends with a variable recording syntax. It is therefore flexible enough to reflect a variety of theoretical justifications for variable harmonization. Using the socio-demographic variable 'marital status', we demonstrate how the CharmStats workflow collates metadata while being guided by the scientific standards of transparency and replication. It encourages researchers to publish their harmonization work by providing researchers who complete the peer review process a permanent identifier. Those who contribute original data harmonization work to their discipline can now be credited through citations. Finally, we propose peer-review standards for harmonization documentation, describe a route to online publishing, and provide a referencing format to cite harmonization projects. Although CharmStats products are designed for social scientists our adherence to the scientific method ensures our products can be used by researchers across the

  13. A Quick Test of Cognitive Speed: norm-referenced criteria for 121 Italian adults aged 45 to 90 years.

    Science.gov (United States)

    Petrazzuoli, Ferdinando; Palmqvist, Sebastian; Thulesius, Hans; Buono, Nicola; Pirrotta, Enzo; Cuffari, Alfredo; Cambielli, Marco; D'Urso, Maurizio; Farinaro, Carmine; Chiumeo, Francesco; Marsala, Valerio; Wiig, Elisabeth H

    2014-05-09

    ABSTRACT Background: A Quick Test of Cognitive Speed (AQT) is a brief test that can identify cognitive impairment. AQT has been validated in Arabic, English, Greek, Japanese, Norwegian, Spanish, and Swedish. The aim of this study was to develop Italian criterion-referenced norms for AQT. Methods: AQT consists of three test plates where the patient shall rapidly name (1) the color of 40 blue, red, yellow, or black squares (AQT color), (2) the form of 40 black figures (circles, squares, triangles, or rectangles; AQT form), (3) the color and form of 40 figures (consisting of previous colors and forms; AQT color-form). The AQT test was administered to 121 Italian cognitively healthy primary care patients (age range: 45-90 years). Their mean Mini-Mental State Examination (MMSE) score was 28.8 ± 0.9 points (range 26-30 points). AQT naming times in seconds were used for developing preliminary criterion cut-off times for different age groups. Results: Age was found to have a significant moderate positive correlation with AQT naming times color (r = 0.65, p color-form (r = 0.63, p color (r = -0.16, p = ns), form (r = -0.24, p = 0.007), and color-form (r = -0.19, p = 0.005). We established preliminary cut-off times for the AQT test based on +1 and +2 standard deviations according to the approach in other languages and settings. Conclusions: This is the first Italian normative AQT study. Future studies of AQT - a test useful for dementia screening in primary care - will eventually refine cut-off times for normality balancing sensitivity and specificity in cognitive diagnostics.

  14. Does a combined dialogic and print referencing reading program improve the vocabulary and print knowledge of children aged 4-5?

    OpenAIRE

    Blakemore, Ms Maria

    2015-01-01

    Dialogic reading (Whitehurst et al., 1988) has a positive effect on the vocabulary of young children (Whitehurst et al., 1994). Knowledge of print is a strong predictor of later reading ability (McCardle et al., 2001). Adults using a print referencing style refer explicitly to aspects of the printed word (Justice & Ezell, 2004). Justice et al. (2009a) recommended coupling the reading styles to see if their simultaneous use could improve both the vocabulary and print knowledge of young child...

  15. Tendencias actuales de citación en los trabajos de investigación filosófica Modern referencing trends in philosophical research papers

    OpenAIRE

    Gemma Muñoz-Alonso López

    2006-01-01

    El artículo propone unificar los criterios para citar y elaborar bibliografías en la investigación en filosofía y en ciencias humanas. Se analizan las ventajas y los inconvenientes del sistema tradicional y del sistema Harvard.The paper attempts to unify criteria for referencing documents and elaborating bibliographies in philosophy and human sciences research. The advantages and disadvantages of the Harvard system are confronted with more traditional methods.

  16. Retrospective chart review of a referenced EEG database in assisting medication selection for treatment of depression in patients with eating disorders

    Directory of Open Access Journals (Sweden)

    Greenblatt JM

    2011-09-01

    Full Text Available James M Greenblatt1, Craig Sussman1, Mariko Jameson1, Lee Yuan1, Daniel A Hoffman2, Dan V Iosifescu31Comprehensive Psychiatric Resources, Waltham, MA, USA; 2Neuro-Therapy Clinic Inc, Denver, CO, USA; 3Mood and Anxiety Disorders Program, Mount Sinai School of Medicine, New York, NY, USABackground: A retrospective chart review was undertaken in a private clinic to examine the clinical outcomes for patients with an eating disorder comorbid with depression or bipolar illness who underwent a referenced electroencephalographic (EEG database analysis to help guide medication selection.Method: We examined 33 charts for patients with the primary psychiatric diagnosis of an eating disorder and comorbid major depressive disorder or bipolar disorder who underwent a quantitative EEG database assessment to provide additional information for choices of medication. The current analysis includes data from 22 subjects who accepted treatments based on information from the referenced-EEG medication database. Hamilton Depression Rating Scale, Clinical Global Impression-Severity, Clinical Global Impression-Improvement, and hospitalization data were examined for these patients.Results: Patients whose EEG data was used for clinical treatment reported significant decreases in associated depressive symptoms (HDRS scores, overall severity of illness (Clinical Global Impression-Severity, and overall clinical global improvement (Clinical Global Impression-Improvement. This cohort also reported fewer inpatient, residential, and partial hospitalization program days following referenced-EEG compared with the two-year period prior to treatment.Conclusion: These findings are consistent with previously reported data for patients with eating disorders and suggest the need for future studies using EEG data correlated with those from other patients with similar quantitative EEG features.Keywords: eating disorders, anorexia, bulimia, depression, referenced-EEG, chart review

  17. Towards an Automatic Framework for Urban Settlement Mapping from Satellite Images: Applications of Geo-referenced Social Media and One Class Classification

    Science.gov (United States)

    Miao, Zelang

    2017-04-01

    Currently, urban dwellers comprise more than half of the world's population and this percentage is still dramatically increasing. The explosive urban growth over the next two decades poses long-term profound impact on people as well as the environment. Accurate and up-to-date delineation of urban settlements plays a fundamental role in defining planning strategies and in supporting sustainable development of urban settlements. In order to provide adequate data about urban extents and land covers, classifying satellite data has become a common practice, usually with accurate enough results. Indeed, a number of supervised learning methods have proven effective in urban area classification, but they usually depend on a large amount of training samples, whose collection is a time and labor expensive task. This issue becomes particularly serious when classifying large areas at the regional/global level. As an alternative to manual ground truth collection, in this work we use geo-referenced social media data. Cities and densely populated areas are an extremely fertile land for the production of individual geo-referenced data (such as GPS and social network data). Training samples derived from geo-referenced social media have several advantages: they are easy to collect, usually they are freely exploitable; and, finally, data from social media are spatially available in many locations, and with no doubt in most urban areas around the world. Despite these advantages, the selection of training samples from social media meets two challenges: 1) there are many duplicated points; 2) method is required to automatically label them as "urban/non-urban". The objective of this research is to validate automatic sample selection from geo-referenced social media and its applicability in one class classification for urban extent mapping from satellite images. The findings in this study shed new light on social media applications in the field of remote sensing.

  18. Criterion-referenced evaluation of day one clinical competencies of veterinary students: VOLES-the VMTH (Veterinary Medicine Teaching Hospital) Online Evaluation System.

    Science.gov (United States)

    Zeck, Steven; Wall, Judy A; Smith, Bradford P; Wilson, W David; Walsh, Donal A

    2012-01-01

    This article describes an extensive online criterion-referenced evaluation system for the assessment of veterinary students' achievement during their final year's Doctor of Veterinary Medicine (or equivalent) clinical education. Data are reported for the 2001 to 2009 University of California at Davis veterinary graduates, for a total of more than 1,100 students. These criterion-referenced evaluations extensively document the level of clinical skills attained and demonstrated during the individual clinical rotations that comprise the fourth-year curriculum. On average, in each of the 17,500 clinical rotations undertaken during this time period, student performance was assessed in at least 11 separate areas of skills, knowledge, and professional attributes. This provided more than 200,000 criterion-referenced judgments of the individual clinical attributes of graduates over nine years. The system is based on a previously detailed and validated definition of the skills, knowledge, and professional attributes that students should have demonstrated before graduation. The extensive database that this system has provided has established that this system, termed VOLES (VMTH [Veterinary Medicine Teaching Hospital] On-Line Evaluation System), is an effective tool to assess the clinical capabilities of veterinary students and their achievement of the "Day One" skills required for entering clinical practice. These expected proficiencies are balanced according to the differing expectations that each area of veterinary clinical practice demands.

  19. Genomics With Cloud Computing

    Directory of Open Access Journals (Sweden)

    Sukhamrit Kaur

    2015-04-01

    Full Text Available Abstract Genomics is study of genome which provides large amount of data for which large storage and computation power is needed. These issues are solved by cloud computing that provides various cloud platforms for genomics. These platforms provides many services to user like easy access to data easy sharing and transfer providing storage in hundreds of terabytes more computational power. Some cloud platforms are Google genomics DNAnexus and Globus genomics. Various features of cloud computing to genomics are like easy access and sharing of data security of data less cost to pay for resources but still there are some demerits like large time needed to transfer data less network bandwidth.

  20. Influence of Electrotactile Tongue Feedback on Controlling Upright Stance during Rotational and/or Translational Sway-referencing with Galvanic Vestibular Stimulation

    Science.gov (United States)

    Wood, Scott J.; Tyler, Mitchell E.; Bach-y-Rita, Paul; MacDougall, Hamish G.; Moore, Steven T.; Stallings, Valerie L.; Paloski, William H.; Black, F. Owen

    2007-01-01

    Integration of multi-sensory inputs to detect tilts relative to gravity is critical for sensorimotor control of upright orientation. Displaying body orientation using electrotactile feedback to the tongue has been developed by Bach-y-Rita and colleagues as a sensory aid to maintain upright stance with impaired vestibular feedback. MacDougall et al. (2006) recently demonstrated that unpredictably varying Galvanic vestibular stimulation (GVS) significantly increased anterior-posterior (AP) sway during rotational sway referencing with eyes closed. The purpose of this study was to assess the influence of electrotactile feedback on postural control performance with pseudorandom binaural bipolar GVS. Postural equilibrium was measured with a computerized hydraulic platform in 10 healthy adults (6M, 4F, 24-65 y). Tactile feedback (TF) of pitch and roll body orientation was derived from a two-axis linear accelerometer mounted on a torso belt and displayed on a 144-point electrotactile array held against the anterior dorsal tongue (BrainPort, Wicab, Inc., Middleton, WI). Subjects were trained to use TF by voluntarily swaying to draw figures on their tongue, both with and without GVS. Subjects were required to keep the intraoral display in their mouths on all trials, including those that did not provide TF. Subjects performed 24 randomized trials (20 s duration with eyes closed) including four support surface conditions (fixed, rotational sway-referenced, translating the support surface proportional to AP sway, and combined rotational-translational sway-referencing), each repeated twice with and without GVS, and with combined GVS and TF. Postural performance was assessed using deviations from upright (peak-to-peak and RMS sway) and convergence toward stability limits (time and distance to base of support boundaries). Postural stability was impaired with GVS in all platform conditions, with larger decrements in performance during trials with rotation sway-referencing

  1. Diet and genomic stability.

    Science.gov (United States)

    Young, Graeme P

    2007-01-01

    Cancer results from a disordered and unstable genome - the degree of abnormality progresses as the process of oncogenesis proceeds. Such genomic instability appears to be subject to control by environmental factors as evidenced by the number of cancers that are either caused by specific environmental agents (lung, skin, cervix) or else regulated by a broader range of agents such as effect of diet on gastric and colorectal cancers. Dietary factors might interact in several ways with the genome to protect against cancer. An agent might interact directly with the genome and regulate expression (as a genetic or epigenetic regulator) or indirectly by influencing DNA 'repair' responses and so improve genomic stability. Research now shows that diet-genomic interactions in cancer go beyond interactions with the normal genome and involve enhancement of normal cellular responses to DNA damage such that genome stability is more effectively maintained. Activation of apoptosis may be a key to protection.

  2. Rat Genome Database (RGD)

    Data.gov (United States)

    U.S. Department of Health & Human Services — The Rat Genome Database (RGD) is a collaborative effort between leading research institutions involved in rat genetic and genomic research to collect, consolidate,...

  3. Exploiting the genome

    Energy Technology Data Exchange (ETDEWEB)

    Block, S. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Cornwall, J. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Dyson, F. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Koonin, S. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Lewis, N. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Schwitters, R. [The MITRE Corporation, McLean, VA (US). JASON Program Office

    1998-09-11

    In 1997, JASON conducted a DOE-sponsored study of the human genome project with special emphasis on the areas of technology, quality assurance and quality control, and informatics. The present study has two aims: first, to update the 1997 Report in light of recent developments in genome sequencing technology, and second, to consider possible roles for the DOE in the ''post-genomic" era, following acquisition of the complete human genome sequence.

  4. Genomic prediction using subsampling

    OpenAIRE

    Xavier, Alencar; Xu, Shizhong; Muir, William; Rainey, Katy Martin

    2017-01-01

    Background Genome-wide assisted selection is a critical tool for the?genetic improvement of plants and animals. Whole-genome regression models in Bayesian framework represent the main family of prediction methods. Fitting such models with a large number of observations involves a prohibitive computational burden. We propose the use of subsampling bootstrap Markov chain in genomic prediction. Such method consists of fitting whole-genome regression models by subsampling observations in each rou...

  5. Ebolavirus comparative genomics

    DEFF Research Database (Denmark)

    Jun, Se-Ran; Leuze, Michael R.; Nookaew, Intawat

    2015-01-01

    The 2014 Ebola outbreak in West Africa is the largest documented for this virus. To examine the dynamics of this genome, we compare more than 100 currently available ebolavirus genomes to each other and to other viral genomes. Based on oligomer frequency analysis, the family Filoviridae forms...

  6. Comparative genomics of Lactobacillus

    Science.gov (United States)

    Kant, Ravi; Blom, Jochen; Palva, Airi; Siezen, Roland J.; de Vos, Willem M.

    2011-01-01

    Summary The genus Lactobacillus includes a diverse group of bacteria consisting of many species that are associated with fermentations of plants, meat or milk. In addition, various lactobacilli are natural inhabitants of the intestinal tract of humans and other animals. Finally, several Lactobacillus strains are marketed as probiotics as their consumption can confer a health benefit to host. Presently, 154 Lactobacillus species are known and a growing fraction of these are subject to draft genome sequencing. However, complete genome sequences are needed to provide a platform for detailed genomic comparisons. Therefore, we selected a total of 20 genomes of various Lactobacillus strains for which complete genomic sequences have been reported. These genomes had sizes varying from 1.8 to 3.3 Mb and other characteristic features, such as G+C content that ranged from 33% to 51%. The Lactobacillus pan genome was found to consist of approximately 14 000 protein‐encoding genes while all 20 genomes shared a total of 383 sets of orthologous genes that defined the Lactobacillus core genome (LCG). Based on advanced phylogeny of the proteins encoded by this LCG, we grouped the 20 strains into three main groups and defined core group genes present in all genomes of a single group, signature group genes shared in all genomes of one group but absent in all other Lactobacillus genomes, and Group‐specific ORFans present in core group genes of one group and absent in all other complete genomes. The latter are of specific value in defining the different groups of genomes. The study provides a platform for present individual comparisons as well as future analysis of new Lactobacillus genomes. PMID:21375712

  7. Ensembl core software resources: storage and programmatic access for DNA sequence and genome annotation.

    Science.gov (United States)

    Ruffier, Magali; Kähäri, Andreas; Komorowska, Monika; Keenan, Stephen; Laird, Matthew; Longden, Ian; Proctor, Glenn; Searle, Steve; Staines, Daniel; Taylor, Kieron; Vullo, Alessandro; Yates, Andrew; Zerbino, Daniel; Flicek, Paul

    2017-01-01

    The Ensembl software resources are a stable infrastructure to store, access and manipulate genome assemblies and their functional annotations. The Ensembl 'Core' database and Application Programming Interface (API) was our first major piece of software infrastructure and remains at the centre of all of our genome resources. Since its initial design more than fifteen years ago, the number of publicly available genomic, transcriptomic and proteomic datasets has grown enormously, accelerated by continuous advances in DNA-sequencing technology. Initially intended to provide annotation for the reference human genome, we have extended our framework to support the genomes of all species as well as richer assembly models. Cross-referenced links to other informatics resources facilitate searching our database with a variety of popular identifiers such as UniProt and RefSeq. Our comprehensive and robust framework storing a large diversity of genome annotations in one location serves as a platform for other groups to generate and maintain their own tailored annotation. We welcome reuse and contributions: our databases and APIs are publicly available, all of our source code is released with a permissive Apache v2.0 licence at http://github.com/Ensembl and we have an active developer mailing list ( http://www.ensembl.org/info/about/contact/index.html ). http://www.ensembl.org. © The Author(s) 2017. Published by Oxford University Press.

  8. A genome blogger manifesto

    Directory of Open Access Journals (Sweden)

    Corpas Manuel

    2012-10-01

    Full Text Available Abstract Cheap prices for genomic testing have revolutionized consumers’ access to personal genomics. Exploration of personal genomes poses significant challenges for customers wishing to learn beyond provider customer reports. A vibrant community has spontaneously appeared blogging experiences and data as a way to learn about their personal genomes. No set of values has publicly been described to date encapsulating ideals and code of conduct for this community. Here I present a first attempt to address this vacuum based on my own personal experiences as genome blogger.

  9. Causes of genome instability

    DEFF Research Database (Denmark)

    Langie, Sabine A S; Koppen, Gudrun; Desaulniers, Daniel

    2015-01-01

    , genome instability can be defined as an enhanced tendency for the genome to acquire mutations; ranging from changes to the nucleotide sequence to chromosomal gain, rearrangements or loss. This review raises the hypothesis that in addition to known human carcinogens, exposure to low dose of other......Genome instability is a prerequisite for the development of cancer. It occurs when genome maintenance systems fail to safeguard the genome's integrity, whether as a consequence of inherited defects or induced via exposure to environmental agents (chemicals, biological agents and radiation). Thus...... chemicals present in our modern society could contribute to carcinogenesis by indirectly affecting genome stability. The selected chemicals with their mechanisms of action proposed to indirectly contribute to genome instability are: heavy metals (DNA repair, epigenetic modification, DNA damage signaling...

  10. Grand Canyon as a universally accessible virtual field trip for intro Geoscience classes using geo-referenced mobile game technology

    Science.gov (United States)

    Bursztyn, N.; Pederson, J. L.; Shelton, B.

    2012-12-01

    There is a well-documented and nationally reported trend of declining interest, poor preparedness, and lack of diversity within U.S. students pursuing geoscience and other STEM disciplines. We suggest that a primary contributing factor to this problem is that introductory geoscience courses simply fail to inspire (i.e. they are boring). Our experience leads us to believe that the hands-on, contextualized learning of field excursions are often the most impactful component of lower division geoscience classes. However, field trips are becoming increasingly more difficult to run due to logistics and liability, high-enrollments, decreasing financial and administrative support, and exclusivity of the physically disabled. Recent research suggests that virtual field trips can be used to simulate this contextualized physical learning through the use of mobile devices - technology that exists in most students' hands already. Our overarching goal is to enhance interest in introductory geoscience courses by providing the kinetic and physical learning experience of field trips through geo-referenced educational mobile games and test the hypothesis that these experiences can be effectively simulated through virtual field trips. We are doing this by developing "serious" games for mobile devices that deliver introductory geology material in a fun and interactive manner. Our new teaching strategy will enhance undergraduate student learning in the geosciences, be accessible to students of diverse backgrounds and physical abilities, and be easily incorporated into higher education programs and curricula at institutions globally. Our prototype involves students virtually navigating downstream along a scaled down Colorado River through Grand Canyon - physically moving around their campus quad, football field or other real location, using their smart phone or a tablet. As students reach the next designated location, a photo or video in Grand Canyon appears along with a geological

  11. Genomic research in Eucalyptus.

    Science.gov (United States)

    Poke, Fiona S; Vaillancourt, René E; Potts, Brad M; Reid, James B

    2005-09-01

    Eucalyptus L'Hérit. is a genus comprised of more than 700 species that is of vital importance ecologically to Australia and to the forestry industry world-wide, being grown in plantations for the production of solid wood products as well as pulp for paper. With the sequencing of the genomes of Arabidopsis thaliana and Oryza sativa and the recent completion of the first tree genome sequence, Populus trichocarpa, attention has turned to the current status of genomic research in Eucalyptus. For several eucalypt species, large segregating families have been established, high-resolution genetic maps constructed and large EST databases generated. Collaborative efforts have been initiated for the integration of diverse genomic projects and will provide the framework for future research including exploiting the sequence of the entire eucalypt genome which is currently being sequenced. This review summarises the current position of genomic research in Eucalyptus and discusses the direction of future research.

  12. Bioinformatics decoding the genome

    CERN Multimedia

    CERN. Geneva; Deutsch, Sam; Michielin, Olivier; Thomas, Arthur; Descombes, Patrick

    2006-01-01

    Extracting the fundamental genomic sequence from the DNA From Genome to Sequence : Biology in the early 21st century has been radically transformed by the availability of the full genome sequences of an ever increasing number of life forms, from bacteria to major crop plants and to humans. The lecture will concentrate on the computational challenges associated with the production, storage and analysis of genome sequence data, with an emphasis on mammalian genomes. The quality and usability of genome sequences is increasingly conditioned by the careful integration of strategies for data collection and computational analysis, from the construction of maps and libraries to the assembly of raw data into sequence contigs and chromosome-sized scaffolds. Once the sequence is assembled, a major challenge is the mapping of biologically relevant information onto this sequence: promoters, introns and exons of protein-encoding genes, regulatory elements, functional RNAs, pseudogenes, transposons, etc. The methodological ...

  13. Genome packaging in viruses

    OpenAIRE

    Sun, Siyang; Rao, Venigalla B.; Rossmann, Michael G.

    2010-01-01

    Genome packaging is a fundamental process in a viral life cycle. Many viruses assemble preformed capsids into which the genomic material is subsequently packaged. These viruses use a packaging motor protein that is driven by the hydrolysis of ATP to condense the nucleic acids into a confined space. How these motor proteins package viral genomes had been poorly understood until recently, when a few X-ray crystal structures and cryo-electron microscopy structures became available. Here we discu...

  14. Fungal Genomics Program

    Energy Technology Data Exchange (ETDEWEB)

    Grigoriev, Igor

    2012-03-12

    The JGI Fungal Genomics Program aims to scale up sequencing and analysis of fungal genomes to explore the diversity of fungi important for energy and the environment, and to promote functional studies on a system level. Combining new sequencing technologies and comparative genomics tools, JGI is now leading the world in fungal genome sequencing and analysis. Over 120 sequenced fungal genomes with analytical tools are available via MycoCosm (www.jgi.doe.gov/fungi), a web-portal for fungal biologists. Our model of interacting with user communities, unique among other sequencing centers, helps organize these communities, improves genome annotation and analysis work, and facilitates new larger-scale genomic projects. This resulted in 20 high-profile papers published in 2011 alone and contributing to the Genomics Encyclopedia of Fungi, which targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts). Our next grand challenges include larger scale exploration of fungal diversity (1000 fungal genomes), developing molecular tools for DOE-relevant model organisms, and analysis of complex systems and metagenomes.

  15. Evolutionary genomics of Entamoeba

    Science.gov (United States)

    Weedall, Gareth D.; Hall, Neil

    2011-01-01

    Entamoeba histolytica is a human pathogen that causes amoebic dysentery and leads to significant morbidity and mortality worldwide. Understanding the genome and evolution of the parasite will help explain how, when and why it causes disease. Here we review current knowledge about the evolutionary genomics of Entamoeba: how differences between the genomes of different species may help explain different phenotypes, and how variation among E. histolytica parasites reveals patterns of population structure. The imminent expansion of the amount genome data will greatly improve our knowledge of the genus and of pathogenic species within it. PMID:21288488

  16. Genomics of Clostridium tetani.

    Science.gov (United States)

    Brüggemann, Holger; Brzuszkiewicz, Elzbieta; Chapeton-Montes, Diana; Plourde, Lucile; Speck, Denis; Popoff, Michel R

    2015-05-01

    Genomic information about Clostridium tetani, the causative agent of the tetanus disease, is scarce. The genome of strain E88, a strain used in vaccine production, was sequenced about 10 years ago. One additional genome (strain 12124569) has recently been released. Here we report three new genomes of C. tetani and describe major differences among all five C. tetani genomes. They all harbor tetanus-toxin-encoding plasmids that contain highly conserved genes for TeNT (tetanus toxin), TetR (transcriptional regulator of TeNT) and ColT (collagenase), but substantially differ in other plasmid regions. The chromosomes share a large core genome that contains about 85% of all genes of a given chromosome. The non-core chromosome comprises mainly prophage-like genomic regions and genes encoding environmental interaction and defense functions (e.g. surface proteins, restriction-modification systems, toxin-antitoxin systems, CRISPR/Cas systems) and other fitness functions (e.g. transport systems, metabolic activities). This new genome information will help to assess the level of genome plasticity of the species C. tetani and provide the basis for detailed comparative studies. Copyright © 2015 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

  17. A spatially referenced regression model (SPARROW) for suspended sediment in streams of the conterminous U.S.

    Science.gov (United States)

    Schwarz, Gregory E.; Smith, Richard A.; Alexander, Richard B.; Gray, John R.

    2001-01-01

    little direct evidence is available concerning the fate of sediment. The common practice of quantifying sediment fate with a sediment delivery ratio, estimated from a simple empirical relation with upstream basin area, does not articulate the relative importance of individual storage sites within a basin (Wolman, 1977). Rates of sediment deposition in reservoirs and flood plains can be determined from empirical measurements, but only a limited number of sites have been monitored, and net rates of deposition or loss from other potential sinks and sources is largely unknown (Stallard, 1998). In particular, little is known about how much sediment loss from fields ultimately makes its way to stream channels, and how much sediment is subsequently stored in or lost from the streambed (Meade and Parker, 1985, Trimble and Crosson, 2000).This paper reports on recent progress made to address empirically the question of sediment fate and transport on a national scale. The model presented here is based on the SPAtially Referenced Regression On Watershed attributes (SPARROW) methodology, first used to estimate the distribution of nutrients in streams and rivers of the United States, and subsequently shown to describe land and stream processes affecting the delivery of nutrients (Smith and others, 1997, Alexander and others, 2000, Preston and Brakebill, 1999). The model makes use of numerous spatial datasets, available at the national level, to explain long-term sediment water-quality conditions in major streams and rivers throughout the United States. Sediment sources are identified using sediment erosion rates from the National Resources Inventory (NRI) (Natural Resources Conservation Service, 2000) and apportioned over the landscape according to 30- meter resolution land-use information from the National Land Cover Data set (NLCD) (U.S. Geological Survey, 2000a). More than 76,000 reservoirs from the National Inventory of Dams (NID) (U.S. Army Corps of Engineers, 1996) are

  18. The Lexicographic Treatment of the Demonstrative Copulative in Sesotho sa Leboa ? An Exercise in Multiple Cross-referencing

    Directory of Open Access Journals (Sweden)

    Gilles-Maurice de Schryver

    2011-10-01

    Full Text Available

    Abstract: In this research article an in-depth investigation is presented of the lexicographictreatment of the demonstrative copulative (DC in Sesotho sa Leboa. This one case study serves asan example to illustrate the so-called 'paradigmatic lemmatisation' of closed-class words in theAfrican languages. The need for such an approach follows a discussion, in Sections 1 and 2 respectively,of the present and missing directions in African-language metalexicography. A theoreticalconspectus of the DC in Sesotho sa Leboa is then offered in Section 3, while Section 4 examines thetreatment of the DC in the four existing desktop dictionaries for this language. The outcomes fromthe two latter sections are then used in Section 5, which analyses the problems of and options for asound lexicographic treatment of the DC in bilingual and monolingual dictionaries. The next twosections proceed with a review of the practical implementation of the DC lemmatisation suggestionsin PyaSsaL, i.e. the Pukuntšutlhaloši ya Sesotho sa Leboa 'Explanatory Sesotho sa Leboa Dictionary'— with Section 6 focussing on the hardcopy and Section 7 on the online version. In the process,the very first fully monolingual African-language dictionary on the Internet is introduced. Section8, finally, concludes briefly.

    Keywords: LEXICOGRAPHY, PARADIGMATIC LEMMATISATION, AFRICAN LANGUAGES,SESOTHO SA LEBOA (NORTHERN SOTHO, SEPEDI, DEMONSTRATIVE COPULATIVE,CROSS-REFERENCING, CORPUS, MONOLINGUAL DICTIONARY, BILINGUAL DICTIONARY, HARDCOPY, ONLINE, INTERNET, EXPLANATORY SESOTHO SA LEBOA DICTIONARY(PYASSAL, SIMULTANEOUS FEEDBACK (SF

    Senaganwa: Tokelotlhalošo ya lešalašupi-leba ka mo pukuntšung ya Sesothosa Leboa — Tirišo ka go šupana go gontši. Ka go sengwalwana se sa nyakišišo,nyakišišo yeo e tseneletšego e laetšwa ka ga go lokelwa le go hlalošwa ga lešalašupi-leba ka mopukuntšung ya Sesotho sa Leboa. Thutwana ya mohuta wo ya nyakišišo e šoma bjalo ka

  19. Computational genomics of hyperthermophiles

    NARCIS (Netherlands)

    Werken, van de H.J.G.

    2008-01-01

    With the ever increasing number of completely sequenced prokaryotic genomes and the subsequent use of functional genomics tools, e.g. DNA microarray and proteomics, computational data analysis and the integration of microbial and molecular data is inevitable. This thesis describes the computational

  20. The Lotus japonicus genome

    DEFF Research Database (Denmark)

    , carbon/nitrogen and secondary metabolism, as well as advances made in high-throughput genomic and genetic approaches. Research focusing on model plants has underpinned the recent growth in plant genomics and genetics and provided a basis for investigations of major crop species. In the legume family...

  1. Phanerochaete chrysosporium genomics

    Science.gov (United States)

    Luis F. Larrondo; Rafael Vicuna; Dan Cullen

    2005-01-01

    A high quality draft genome sequence has been generated for the lignocellulose-degrading basidiomycete Phanerochaete chrysosporium (Martinez et al. 2004). Analysis of the genome in the context of previously established genetics and physiology is presented. Transposable elements and their potential relationship to genes involved in lignin degradation are systematically...

  2. Genome-Scale Models

    DEFF Research Database (Denmark)

    Bergdahl, Basti; Sonnenschein, Nikolaus; Machado, Daniel

    2016-01-01

    An introduction to genome-scale models, how to build and use them, will be given in this chapter. Genome-scale models have become an important part of systems biology and metabolic engineering, and are increasingly used in research, both in academica and in industry, both for modeling chemical pr...

  3. Safeguarding genome integrity

    DEFF Research Database (Denmark)

    Sørensen, Claus Storgaard; Syljuåsen, Randi G

    2012-01-01

    Mechanisms that preserve genome integrity are highly important during the normal life cycle of human cells. Loss of genome protective mechanisms can lead to the development of diseases such as cancer. Checkpoint kinases function in the cellular surveillance pathways that help cells to cope with DNA...

  4. Human genome I

    International Nuclear Information System (INIS)

    Anon.

    1989-01-01

    An international conference, Human Genome I, was held Oct. 2-4, 1989 in San Diego, Calif. Selected speakers discussed: Current Status of the Genome Project; Technique Innovations; Interesting regions; Applications; and Organization - Different Views of Current and Future Science and Procedures. Posters, consisting of 119 presentations, were displayed during the sessions. 119 were indexed for inclusion to the Energy Data Base

  5. Breeding-assisted genomics.

    Science.gov (United States)

    Poland, Jesse

    2015-04-01

    The revolution of inexpensive sequencing has ushered in an unprecedented age of genomics. The promise of using this technology to accelerate plant breeding is being realized with a vision of genomics-assisted breeding that will lead to rapid genetic gain for expensive and difficult traits. The reality is now that robust phenotypic data is an increasing limiting resource to complement the current wealth of genomic information. While genomics has been hailed as the discipline to fundamentally change the scope of plant breeding, a more symbiotic relationship is likely to emerge. In the context of developing and evaluating large populations needed for functional genomics, none excel in this area more than plant breeders. While genetic studies have long relied on dedicated, well-structured populations, the resources dedicated to these populations in the context of readily available, inexpensive genotyping is making this philosophy less tractable relative to directly focusing functional genomics on material in breeding programs. Through shifting effort for basic genomic studies from dedicated structured populations, to capturing the entire scope of genetic determinants in breeding lines, we can move towards not only furthering our understanding of functional genomics in plants, but also rapidly improving crops for increased food security, availability and nutrition. Copyright © 2015 Elsevier Ltd. All rights reserved.

  6. Musa sebagai Model Genom

    Directory of Open Access Journals (Sweden)

    RITA MEGIA

    2005-12-01

    Full Text Available During the meeting in Arlington, USA in 2001, the scientists grouped in PROMUSA agreed with the launching of the Global Musa Genomics Consortium. The Consortium aims to apply genomics technologies to the improvement of this important crop. These genome projects put banana as the third model species after Arabidopsis and rice that will be analyzed and sequenced. Comparing to Arabidopsis and rice, banana genome provides a unique and powerful insight into structural and in functional genomics that could not be found in those two species. This paper discussed these subjects-including the importance of banana as the fourth main food in the world, the evolution and biodiversity of this genetic resource and its parasite.

  7. Genomic Prediction in Barley

    DEFF Research Database (Denmark)

    Edriss, Vahid; Cericola, Fabio; Jensen, Jens D

    2015-01-01

    Genomic prediction uses markers (SNPs) across the whole genome to predict individual breeding values at an early growth stage potentially before large scale phenotyping. One of the applications of genomic prediction in plant breeding is to identify the best individual candidate lines to contribute...... to next generation. The main goal of this study was to see the potential of using genomic prediction in a commercial Barley breeding program. The data used in this study was from Nordic Seed company which is located in Denmark. Around 350 advanced lines were genotyped with 9K Barely chip from Illumina....... Traits used in this study were grain yield, plant height and heading date. Heading date is number days it takes after 1st June for plant to head. Heritabilities were 0.33, 0.44 and 0.48 for yield, height and heading, respectively for the average of nine plots. The GBLUP model was used for genomic...

  8. The genome editing revolution

    DEFF Research Database (Denmark)

    Stella, Stefano; Montoya, Guillermo

    2016-01-01

    -Cas system has become the main tool for genome editing in many laboratories. Currently the targeted genome editing technology has been used in many fields and may be a possible approach for human gene therapy. Furthermore, it can also be used to modifying the genomes of model organisms for studying human......In the last 10 years, we have witnessed a blooming of targeted genome editing systems and applications. The area was revolutionized by the discovery and characterization of the transcription activator-like effector proteins, which are easier to engineer to target new DNA sequences than...... sequence). This ribonucleoprotein complex protects bacteria from invading DNAs, and it was adapted to be used in genome editing. The CRISPR ribonucleic acid (RNA) molecule guides to the specific DNA site the Cas9 nuclease to cleave the DNA target. Two years and more than 1000 publications later, the CRISPR...

  9. Phytozome Comparative Plant Genomics Portal

    Energy Technology Data Exchange (ETDEWEB)

    Goodstein, David; Batra, Sajeev; Carlson, Joseph; Hayes, Richard; Phillips, Jeremy; Shu, Shengqiang; Schmutz, Jeremy; Rokhsar, Daniel

    2014-09-09

    The Dept. of Energy Joint Genome Institute is a genomics user facility supporting DOE mission science in the areas of Bioenergy, Carbon Cycling, and Biogeochemistry. The Plant Program at the JGI applies genomic, analytical, computational and informatics platforms and methods to: 1. Understand and accelerate the improvement (domestication) of bioenergy crops 2. Characterize and moderate plant response to climate change 3. Use comparative genomics to identify constrained elements and infer gene function 4. Build high quality genomic resource platforms of JGI Plant Flagship genomes for functional and experimental work 5. Expand functional genomic resources for Plant Flagship genomes

  10. Personal genomes, participatory genomics and the anonymity ...

    Indian Academy of Sciences (India)

    2014-12-02

    Dec 2, 2014 ... gies which have enabled miniaturization, large-scale paral- lelization and improved readout coupled with highly scala- ble data capture and analysis tools, commonly known as. 'next generation' sequencing technologies (Mardis 2008). The cost of whole genome sequencing has been expected to be as ...

  11. The Banana Genome Hub

    Science.gov (United States)

    Droc, Gaëtan; Larivière, Delphine; Guignon, Valentin; Yahiaoui, Nabila; This, Dominique; Garsmeur, Olivier; Dereeper, Alexis; Hamelin, Chantal; Argout, Xavier; Dufayard, Jean-François; Lengelle, Juliette; Baurens, Franc-Christophe; Cenci, Alberto; Pitollat, Bertrand; D’Hont, Angélique; Ruiz, Manuel; Rouard, Mathieu; Bocs, Stéphanie

    2013-01-01

    Banana is one of the world’s favorite fruits and one of the most important crops for developing countries. The banana reference genome sequence (Musa acuminata) was recently released. Given the taxonomic position of Musa, the completed genomic sequence has particular comparative value to provide fresh insights about the evolution of the monocotyledons. The study of the banana genome has been enhanced by a number of tools and resources that allows harnessing its sequence. First, we set up essential tools such as a Community Annotation System, phylogenomics resources and metabolic pathways. Then, to support post-genomic efforts, we improved banana existing systems (e.g. web front end, query builder), we integrated available Musa data into generic systems (e.g. markers and genetic maps, synteny blocks), we have made interoperable with the banana hub, other existing systems containing Musa data (e.g. transcriptomics, rice reference genome, workflow manager) and finally, we generated new results from sequence analyses (e.g. SNP and polymorphism analysis). Several uses cases illustrate how the Banana Genome Hub can be used to study gene families. Overall, with this collaborative effort, we discuss the importance of the interoperability toward data integration between existing information systems. Database URL: http://banana-genome.cirad.fr/ PMID:23707967

  12. Chromatographic separation and continuously referenced, on-line monitoring of creatine kinase isoenzymes by use of an immobilized-enzyme microreactor

    International Nuclear Information System (INIS)

    Denton, M.S.; Bostick, W.D.; Dinsmore, S.R.; Mrochek, J.E.

    1978-01-01

    We describe a new concept in continuously referenced monitoring of the isoenzyme activities of creatine kinase (EC 2.7.3.2) after liquid-chromatographic separation. After separation on a diethylaminoethyl-Sephacel column, the three isoenzymes of creatine kinase undergo a series of upled enzyme reactions, ultimately resulting in the formation of ultraviolet-detectable NADPH. A major advantage of this detection system is the immobilized-enzyme microreactor (2 x 17 mm), which may be removed and stored refrigerated when not in use. A split-stream configuration allows self-blanking of endogenous ultraviolet-absorbing constituents in authentic sera samples, which would otherwise make definitive diagnosis and quantitation difficult or impossible. This detection system is applicable to the automated analysis of creatine kinase isoenzymes in the clinical laboratory. 5 figures; 42 references

  13. Genomic signal processing

    CERN Document Server

    Shmulevich, Ilya

    2007-01-01

    Genomic signal processing (GSP) can be defined as the analysis, processing, and use of genomic signals to gain biological knowledge, and the translation of that knowledge into systems-based applications that can be used to diagnose and treat genetic diseases. Situated at the crossroads of engineering, biology, mathematics, statistics, and computer science, GSP requires the development of both nonlinear dynamical models that adequately represent genomic regulation, and diagnostic and therapeutic tools based on these models. This book facilitates these developments by providing rigorous mathema

  14. Genomic taxonomy of vibrios

    Directory of Open Access Journals (Sweden)

    Iida Tetsuya

    2009-10-01

    Full Text Available Abstract Background Vibrio taxonomy has been based on a polyphasic approach. In this study, we retrieve useful taxonomic information (i.e. data that can be used to distinguish different taxonomic levels, such as species and genera from 32 genome sequences of different vibrio species. We use a variety of tools to explore the taxonomic relationship between the sequenced genomes, including Multilocus Sequence Analysis (MLSA, supertrees, Average Amino Acid Identity (AAI, genomic signatures, and Genome BLAST atlases. Our aim is to analyse the usefulness of these tools for species identification in vibrios. Results We have generated four new genome sequences of three Vibrio species, i.e., V. alginolyticus 40B, V. harveyi-like 1DA3, and V. mimicus strains VM573 and VM603, and present a broad analyses of these genomes along with other sequenced Vibrio species. The genome atlas and pangenome plots provide a tantalizing image of the genomic differences that occur between closely related sister species, e.g. V. cholerae and V. mimicus. The vibrio pangenome contains around 26504 genes. The V. cholerae core genome and pangenome consist of 1520 and 6923 genes, respectively. Pangenomes might allow different strains of V. cholerae to occupy different niches. MLSA and supertree analyses resulted in a similar phylogenetic picture, with a clear distinction of four groups (Vibrio core group, V. cholerae-V. mimicus, Aliivibrio spp., and Photobacterium spp.. A Vibrio species is defined as a group of strains that share > 95% DNA identity in MLSA and supertree analysis, > 96% AAI, ≤ 10 genome signature dissimilarity, and > 61% proteome identity. Strains of the same species and species of the same genus will form monophyletic groups on the basis of MLSA and supertree. Conclusion The combination of different analytical and bioinformatics tools will enable the most accurate species identification through genomic computational analysis. This endeavour will culminate in

  15. Traditional medicine and genomics

    Directory of Open Access Journals (Sweden)

    Kalpana Joshi

    2010-01-01

    Full Text Available ′Omics′ developments in the form of genomics, proteomics and metabolomics have increased the impetus of traditional medicine research. Studies exploring the genomic, proteomic and metabolomic basis of human constitutional types based on Ayurveda and other systems of oriental medicine are becoming popular. Such studies remain important to developing better understanding of human variations and individual differences. Countries like India, Korea, China and Japan are investing in research on evidence-based traditional medicines and scientific validation of fundamental principles. This review provides an account of studies addressing relationships between traditional medicine and genomics.

  16. Traditional medicine and genomics.

    Science.gov (United States)

    Joshi, Kalpana; Ghodke, Yogita; Shintre, Pooja

    2010-01-01

    'Omics' developments in the form of genomics, proteomics and metabolomics have increased the impetus of traditional medicine research. Studies exploring the genomic, proteomic and metabolomic basis of human constitutional types based on Ayurveda and other systems of oriental medicine are becoming popular. Such studies remain important to developing better understanding of human variations and individual differences. Countries like India, Korea, China and Japan are investing in research on evidence-based traditional medicines and scientific validation of fundamental principles. This review provides an account of studies addressing relationships between traditional medicine and genomics.

  17. Human Genome Program

    Energy Technology Data Exchange (ETDEWEB)

    1993-01-01

    The DOE Human Genome program has grown tremendously, as shown by the marked increase in the number of genome-funded projects since the last workshop held in 1991. The abstracts in this book describe the genome research of DOE-funded grantees and contractors and invited guests, and all projects are represented at the workshop by posters. The 3-day meeting includes plenary sessions on ethical, legal, and social issues pertaining to the availability of genetic data; sequencing techniques, informatics support; and chromosome and cDNA mapping and sequencing.

  18. What Is a Genome?

    Directory of Open Access Journals (Sweden)

    Aaron David Goldman

    2016-07-01

    Full Text Available The genome is often described as the information repository of an organism. Whether millions or billions of letters of DNA, its transmission across generations confers the principal medium for inheritance of organismal traits. Several emerging areas of research demonstrate that this definition is an oversimplification. Here, we explore ways in which a deeper understanding of genomic diversity and cell physiology is challenging the concepts of physical permanence attached to the genome as well as its role as the sole information source for an organism.

  19. Human Genome Project

    Energy Technology Data Exchange (ETDEWEB)

    Block, S. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Cornwall, J. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Dally, W. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Dyson, F. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Fortson, N. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Joyce, G. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Kimble, H. J. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Lewis, N. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Max, C. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Prince, T. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Schwitters, R. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Weinberger, P. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Woodin, W. H. [The MITRE Corporation, McLean, VA (US). JASON Program Office

    1998-01-04

    The study reviews Department of Energy supported aspects of the United States Human Genome Project, the joint National Institutes of Health/Department of Energy program to characterize all human genetic material, to discover the set of human genes, and to render them accessible for further biological study. The study concentrates on issues of technology, quality assurance/control, and informatics relevant to current effort on the genome project and needs beyond it. Recommendations are presented on areas of the genome program that are of particular interest to and supported by the Department of Energy.

  20. Genomic insights into tuberculosis.

    Science.gov (United States)

    Galagan, James E

    2014-05-01

    Prevalent since pre-history, human tuberculosis - caused by the pathogen Mycobacterium tuberculosis - remains a major source of death worldwide. Moreover, increasing drug resistance poses the threat of disease resurgence. However, the expanding application of genomic techniques is providing new avenues for combating this old foe. Whole-genome sequencing, comparative genomics and systems biology are generating new insights into the origins and ongoing evolution of M. tuberculosis, as well as the molecular basis for its pathogenicity. These have important implications for our perspective of the disease, development of new drugs and vaccines, and treatment of patients using existing therapeutics.

  1. Postural Control Can Be Well Maintained by Healthy, Young Adults in Difficult Visual Task, Even in Sway-Referenced Dynamic Conditions.

    Science.gov (United States)

    Lions, Cynthia; Bucci, Maria Pia; Bonnet, Cédrick

    2016-01-01

    To challenge the validity of existing cognitive models of postural control, we recorded eye movements and postural sway during two visual tasks (a control free-viewing task and a difficult searching task), and two postural tasks (one static task in which the platform was maintained stable and a dynamic task in which the platform moved in a sway-referenced manner.) We expected these models to be insufficient to predict the results in postural control both in static-as already shown in the literature reports-and in dynamic platform conditions. Twelve healthy, young adults (17.3 to 34.1 years old) participated in this study. Postural performances were evaluated using the Multitest platform (Framiral®) and ocular recording was performed with Mobile T2 (e(ye)BRAIN®). In the free-viewing task, the participants had to look at an image, without any specific instruction. In the searching task, the participants had to look at an image and also to locate the position of an object in the scene. Postural sway was only significantly higher in the dynamic free-viewing condition than in the three other conditions with no significant difference between these three other conditions. Visual task performance was slightly higher in dynamic than in static conditions. As expected, our results did not confirm the main assumption of the current cognitive models of postural control-i.e. that the limited attentional resources of the brain should explain changes in postural control in our conditions. Indeed, 1) the participants did not sway significantly more in the sway-referenced dynamic searching condition than in any other condition; 2) the participants swayed significantly less in both static and dynamic searching conditions than in the dynamic free-viewing condition. We suggest that a new cognitive model illustrating the adaptive, functional role of the brain to control upright stance is necessary for future studies.

  2. Postural Control Can Be Well Maintained by Healthy, Young Adults in Difficult Visual Task, Even in Sway-Referenced Dynamic Conditions.

    Directory of Open Access Journals (Sweden)

    Cynthia Lions

    Full Text Available To challenge the validity of existing cognitive models of postural control, we recorded eye movements and postural sway during two visual tasks (a control free-viewing task and a difficult searching task, and two postural tasks (one static task in which the platform was maintained stable and a dynamic task in which the platform moved in a sway-referenced manner. We expected these models to be insufficient to predict the results in postural control both in static-as already shown in the literature reports-and in dynamic platform conditions.Twelve healthy, young adults (17.3 to 34.1 years old participated in this study. Postural performances were evaluated using the Multitest platform (Framiral® and ocular recording was performed with Mobile T2 (e(yeBRAIN®. In the free-viewing task, the participants had to look at an image, without any specific instruction. In the searching task, the participants had to look at an image and also to locate the position of an object in the scene.Postural sway was only significantly higher in the dynamic free-viewing condition than in the three other conditions with no significant difference between these three other conditions. Visual task performance was slightly higher in dynamic than in static conditions.As expected, our results did not confirm the main assumption of the current cognitive models of postural control-i.e. that the limited attentional resources of the brain should explain changes in postural control in our conditions. Indeed, 1 the participants did not sway significantly more in the sway-referenced dynamic searching condition than in any other condition; 2 the participants swayed significantly less in both static and dynamic searching conditions than in the dynamic free-viewing condition. We suggest that a new cognitive model illustrating the adaptive, functional role of the brain to control upright stance is necessary for future studies.

  3. Not to put too fine a point on it - does increasing precision of geographic referencing improve species distribution models for a wide-ranging migratory bat?

    Science.gov (United States)

    Hayes, Mark A.; Ozenberger, Katharine; Cryan, Paul M.; Wunder, Michael B.

    2015-01-01

    Bat specimens held in natural history museum collections can provide insights into the distribution of species. However, there are several important sources of spatial error associated with natural history specimens that may influence the analysis and mapping of bat species distributions. We analyzed the importance of geographic referencing and error correction in species distribution modeling (SDM) using occurrence records of hoary bats (Lasiurus cinereus). This species is known to migrate long distances and is a species of increasing concern due to fatalities documented at wind energy facilities in North America. We used 3,215 museum occurrence records collected from 1950–2000 for hoary bats in North America. We compared SDM performance using five approaches: generalized linear models, multivariate adaptive regression splines, boosted regression trees, random forest, and maximum entropy models. We evaluated results using three SDM performance metrics (AUC, sensitivity, and specificity) and two data sets: one comprised of the original occurrence data, and a second data set consisting of these same records after the locations were adjusted to correct for identifiable spatial errors. The increase in precision improved the mean estimated spatial error associated with hoary bat records from 5.11 km to 1.58 km, and this reduction in error resulted in a slight increase in all three SDM performance metrics. These results provide insights into the importance of geographic referencing and the value of correcting spatial errors in modeling the distribution of a wide-ranging bat species. We conclude that the considerable time and effort invested in carefully increasing the precision of the occurrence locations in this data set was not worth the marginal gains in improved SDM performance, and it seems likely that gains would be similar for other bat species that range across large areas of the continent, migrate, and are habitat generalists.

  4. solQTL: a tool for QTL analysis, visualization and linking to genomes at SGN database

    Directory of Open Access Journals (Sweden)

    van der Knaap Esther

    2010-10-01

    Full Text Available Abstract Background A common approach to understanding the genetic basis of complex traits is through identification of associated quantitative trait loci (QTL. Fine mapping QTLs requires several generations of backcrosses and analysis of large populations, which is time-consuming and costly effort. Furthermore, as entire genomes are being sequenced and an increasing amount of genetic and expression data are being generated, a challenge remains: linking phenotypic variation to the underlying genomic variation. To identify candidate genes and understand the molecular basis underlying the phenotypic variation of traits, bioinformatic approaches are needed to exploit information such as genetic map, expression and whole genome sequence data of organisms in biological databases. Description The Sol Genomics Network (SGN, http://solgenomics.net is a primary repository for phenotypic, genetic, genomic, expression and metabolic data for the Solanaceae family and other related Asterids species and houses a variety of bioinformatics tools. SGN has implemented a new approach to QTL data organization, storage, analysis, and cross-links with other relevant data in internal and external databases. The new QTL module, solQTL, http://solgenomics.net/qtl/, employs a user-friendly web interface for uploading raw phenotype and genotype data to the database, R/QTL mapping software for on-the-fly QTL analysis and algorithms for online visualization and cross-referencing of QTLs to relevant datasets and tools such as the SGN Comparative Map Viewer and Genome Browser. Here, we describe the development of the solQTL module and demonstrate its application. Conclusions solQTL allows Solanaceae researchers to upload raw genotype and phenotype data to SGN, perform QTL analysis and dynamically cross-link to relevant genetic, expression and genome annotations. Exploration and synthesis of the relevant data is expected to help facilitate identification of candidate genes

  5. Mouse Genome Informatics (MGI)

    Data.gov (United States)

    U.S. Department of Health & Human Services — MGI is the international database resource for the laboratory mouse, providing integrated genetic, genomic, and biological data to facilitate the study of human...

  6. Rice Genomics: Gene discovery

    Indian Academy of Sciences (India)

    There is a need for discovering candidate genes( a lot of them all over the genome indeed ) and the unlimited allelic variation that can productively take over rice metabolism when cellular water content falls below threshold levels.

  7. Lophotrochozoan mitochondrial genomes

    Energy Technology Data Exchange (ETDEWEB)

    Valles, Yvonne; Boore, Jeffrey L.

    2005-10-01

    Progress in both molecular techniques and phylogeneticmethods has challenged many of the interpretations of traditionaltaxonomy. One example is in the recognition of the animal superphylumLophotrochozoa (annelids, mollusks, echiurans, platyhelminthes,brachiopods, and other phyla), although the relationships within thisgroup and the inclusion of some phyla remain uncertain. While much ofthis progress in phylogenetic reconstruction has been based on comparingsingle gene sequences, we are beginning to see the potential of comparinglarge-scale features of genomes, such as the relative order of genes.Even though tremendous progress is being made on the sequencedetermination of whole nuclear genomes, the dataset of choice forgenome-level characters for many animals across a broad taxonomic rangeremains mitochondrial genomes. We review here what is known aboutmitochondrial genomes of the lophotrochozoans and discuss the promisethat this dataset will enable insight into theirrelationships.

  8. Genomic definition of species

    Energy Technology Data Exchange (ETDEWEB)

    Crkvenjakov, R.; Drmanac, R.

    1991-07-01

    The subject of this paper is the definition of species based on the assumption that genome is the fundamental level for the origin and maintenance of biological diversity. For this view to be logically consistent it is necessary to assume the existence and operation of the new law which we call genome law. For this reason the genome law is included in the explanation of species phenomenon presented here even if its precise formulation and elaboration are left for the future. The intellectual underpinnings of this definition can be traced to Goldschmidt. We wish to explore some philosophical aspects of the definition of species in terms of the genome. The point of proposing the definition on these grounds is that any real advance in evolutionary theory has to be correct in both its philosophy and its science.

  9. The rise of genomics.

    Science.gov (United States)

    Weissenbach, Jean

    2016-01-01

    A brief history of the development of genomics is provided. Complete sequencing of genomes of uni- and multicellular organisms is based on important progress in sequencing and bioinformatics. Evolution of these methods is ongoing and has triggered an explosion in data production and analysis. Initial analyses focused on the inventory of genes encoding proteins. Completeness and quality of gene prediction remains crucial. Genome analyses profoundly modified our views on evolution, biodiversity and contributed to the detection of new functions, yet to be fully elucidated, such as those fulfilled by non-coding RNAs. Genomics has become the basis for the study of biology and provides the molecular support for a bunch of large-scale studies, the omics. Copyright © 2016 Académie des sciences. Published by Elsevier SAS. All rights reserved.

  10. Annotating individual human genomes.

    Science.gov (United States)

    Torkamani, Ali; Scott-Van Zeeland, Ashley A; Topol, Eric J; Schork, Nicholas J

    2011-10-01

    Advances in DNA sequencing technologies have made it possible to rapidly, accurately and affordably sequence entire individual human genomes. As impressive as this ability seems, however, it will not likely amount to much if one cannot extract meaningful information from individual sequence data. Annotating variations within individual genomes and providing information about their biological or phenotypic impact will thus be crucially important in moving individual sequencing projects forward, especially in the context of the clinical use of sequence information. In this paper we consider the various ways in which one might annotate individual sequence variations and point out limitations in the available methods for doing so. It is arguable that, in the foreseeable future, DNA sequencing of individual genomes will become routine for clinical, research, forensic, and personal purposes. We therefore also consider directions and areas for further research in annotating genomic variants. Copyright © 2011 Elsevier Inc. All rights reserved.

  11. ANNOTATING INDIVIDUAL HUMAN GENOMES*

    Science.gov (United States)

    Torkamani, Ali; Scott-Van Zeeland, Ashley A.; Topol, Eric J.; Schork, Nicholas J.

    2014-01-01

    Advances in DNA sequencing technologies have made it possible to rapidly, accurately and affordably sequence entire individual human genomes. As impressive as this ability seems, however, it will not likely to amount to much if one cannot extract meaningful information from individual sequence data. Annotating variations within individual genomes and providing information about their biological or phenotypic impact will thus be crucially important in moving individual sequencing projects forward, especially in the context of the clinical use of sequence information. In this paper we consider the various ways in which one might annotate individual sequence variations and point out limitations in the available methods for doing so. It is arguable that, in the foreseeable future, DNA sequencing of individual genomes will become routine for clinical, research, forensic, and personal purposes. We therefore also consider directions and areas for further research in annotating genomic variants. PMID:21839162

  12. Epidemiology & Genomics Research Program

    Science.gov (United States)

    The Epidemiology and Genomics Research Program, in the National Cancer Institute's Division of Cancer Control and Population Sciences, funds research in human populations to understand the determinants of cancer occurrence and outcomes.

  13. Genomics and fish adaptation

    Directory of Open Access Journals (Sweden)

    Agostinho Antunes

    2015-12-01

    Full Text Available The completion of the human genome sequencing in 2003 opened a new perspective into the importance of whole genome sequencing projects, and currently multiple species are having their genomes completed sequenced, from simple organisms, such as bacteria, to more complex taxa, such as mammals. This voluminous sequencing data generated across multiple organisms provides also the framework to better understand the genetic makeup of such species and related ones, allowing to explore the genetic changes underlining the evolution of diverse phenotypic traits. Here, recent results from our group retrieved from comparative evolutionary genomic analyses of varied fish species will be considered to exemplify how gene novelty and gene enhancement by positive selection might have been determinant in the success of adaptive radiations into diverse habitats and lifestyles.

  14. The human genome project

    International Nuclear Information System (INIS)

    Worton, R.

    1996-01-01

    The Human Genome Project is a massive international research project, costing 3 to 5 billion dollars and expected to take 15 years, which will identify the all the genes in the human genome - i.e. the complete sequence of bases in human DNA. The prize will be the ability to identify genes causing or predisposing to disease, and in some cases the development of gene therapy, but this new knowledge will raise important ethical issues

  15. The Genomic Standards Consortium

    DEFF Research Database (Denmark)

    Field, Dawn; Amaral-Zettler, Linda; Cochrane, Guy

    2011-01-01

    A vast and rich body of information has grown up as a result of the world's enthusiasm for 'omics technologies. Finding ways to describe and make available this information that maximise its usefulness has become a major effort across the 'omics world. At the heart of this effort is the Genomic S...... and quantity of contextual information about our public collections of genomes, metagenomes, and marker gene sequences....

  16. Decoding the human genome

    CERN Document Server

    CERN. Geneva. Audiovisual Unit; Antonerakis, S E

    2002-01-01

    Decoding the Human genome is a very up-to-date topic, raising several questions besides purely scientific, in view of the two competing teams (public and private), the ethics of using the results, and the fact that the project went apparently faster and easier than expected. The lecture series will address the following chapters: Scientific basis and challenges. Ethical and social aspects of genomics.

  17. Human Germline Genome Editing

    OpenAIRE

    Ormond, Kelly E.; Mortlock, Douglas P.; Scholes, Derek T.; Bombard, Yvonne; Brody, Lawrence C.; Faucett, W. Andrew; Garrison, Nanibaa’ A.; Hercher, Laura; Isasi, Rosario; Middleton, Anna; Musunuru, Kiran; Shriner, Daniel; Virani, Alice; Young, Caroline E.

    2017-01-01

    With CRISPR/Cas9 and other genome-editing technologies, successful somatic and germline genome editing are becoming feasible. To respond, an American Society of Human Genetics (ASHG) workgroup developed this position statement, which was approved by the ASHG Board in March 2017. The workgroup included representatives from the UK Association of Genetic Nurses and Counsellors, Canadian Association of Genetic Counsellors, International Genetic Epidemiology Society, and US National Society of Gen...

  18. Molluscan Evolutionary Genomics

    Energy Technology Data Exchange (ETDEWEB)

    Simison, W. Brian; Boore, Jeffrey L.

    2005-12-01

    In the last 20 years there have been dramatic advances in techniques of high-throughput DNA sequencing, most recently accelerated by the Human Genome Project, a program that has determined the three billion base pair code on which we are based. Now this tremendous capability is being directed at other genome targets that are being sampled across the broad range of life. This opens up opportunities as never before for evolutionary and organismal biologists to address questions of both processes and patterns of organismal change. We stand at the dawn of a new 'modern synthesis' period, paralleling that of the early 20th century when the fledgling field of genetics first identified the underlying basis for Darwin's theory. We must now unite the efforts of systematists, paleontologists, mathematicians, computer programmers, molecular biologists, developmental biologists, and others in the pursuit of discovering what genomics can teach us about the diversity of life. Genome-level sampling for mollusks to date has mostly been limited to mitochondrial genomes and it is likely that these will continue to provide the best targets for broad phylogenetic sampling in the near future. However, we are just beginning to see an inroad into complete nuclear genome sequencing, with several mollusks and other eutrochozoans having been selected for work about to begin. Here, we provide an overview of the state of molluscan mitochondrial genomics, highlight a few of the discoveries from this research, outline the promise of broadening this dataset, describe upcoming projects to sequence whole mollusk nuclear genomes, and challenge the community to prepare for making the best use of these data.

  19. Human social genomics.

    Directory of Open Access Journals (Sweden)

    Steven W Cole

    2014-08-01

    Full Text Available A growing literature in human social genomics has begun to analyze how everyday life circumstances influence human gene expression. Social-environmental conditions such as urbanity, low socioeconomic status, social isolation, social threat, and low or unstable social status have been found to associate with differential expression of hundreds of gene transcripts in leukocytes and diseased tissues such as metastatic cancers. In leukocytes, diverse types of social adversity evoke a common conserved transcriptional response to adversity (CTRA characterized by increased expression of proinflammatory genes and decreased expression of genes involved in innate antiviral responses and antibody synthesis. Mechanistic analyses have mapped the neural "social signal transduction" pathways that stimulate CTRA gene expression in response to social threat and may contribute to social gradients in health. Research has also begun to analyze the functional genomics of optimal health and thriving. Two emerging opportunities now stand to revolutionize our understanding of the everyday life of the human genome: network genomics analyses examining how systems-level capabilities emerge from groups of individual socially sensitive genomes and near-real-time transcriptional biofeedback to empirically optimize individual well-being in the context of the unique genetic, geographic, historical, developmental, and social contexts that jointly shape the transcriptional realization of our innate human genomic potential for thriving.

  20. RadGenomics project

    International Nuclear Information System (INIS)

    Iwakawa, Mayumi; Imai, Takashi; Harada, Yoshinobu

    2002-01-01

    Human health is determined by a complex interplay of factors, predominantly between genetic susceptibility, environmental conditions and aging. The ultimate aim of the RadGenomics (Radiation Genomics) project is to understand the implications of heterogeneity in responses to ionizing radiation arising from genetic variation between individuals in the human population. The rapid progression of the human genome sequencing and the recent development of new technologies in molecular genetics are providing us with new opportunities to understand the genetic basis of individual differences in susceptibility to natural and/or artificial environmental factors, including radiation exposure. The RadGenomics project will inevitably lead to improved protocols for personalized radiotherapy and reductions in the potential side effects of such treatment. The project will contribute to future research into the molecular mechanisms of radiation sensitivity in humans and will stimulate the development of new high-throughput technologies for a broader application of biological and medical sciences. The staff members are specialists in a variety of fields, including genome science, radiation biology, medical science, molecular biology, and informatics, and have joined the RadGenomics project from various universities, companies, and research institutes. The project started in April 2001. (author)

  1. How the genome folds

    Science.gov (United States)

    Lieberman Aiden, Erez

    2012-02-01

    I describe Hi-C, a novel technology for probing the three-dimensional architecture of whole genomes by coupling proximity-based ligation with massively parallel sequencing. Working with collaborators at the Broad Institute and UMass Medical School, we used Hi-C to construct spatial proximity maps of the human genome at a resolution of 1Mb. These maps confirm the presence of chromosome territories and the spatial proximity of small, gene-rich chromosomes. We identified an additional level of genome organization that is characterized by the spatial segregation of open and closed chromatin to form two genome-wide compartments. At the megabase scale, the chromatin conformation is consistent with a fractal globule, a knot-free conformation that enables maximally dense packing while preserving the ability to easily fold and unfold any genomic locus. The fractal globule is distinct from the more commonly used globular equilibrium model. Our results demonstrate the power of Hi-C to map the dynamic conformations of whole genomes.

  2. Comparative Genome Viewer

    International Nuclear Information System (INIS)

    Molineris, I.; Sales, G.

    2009-01-01

    The amount of information about genomes, both in the form of complete sequences and annotations, has been exponentially increasing in the last few years. As a result there is the need for tools providing a graphical representation of such information that should be comprehensive and intuitive. Visual representation is especially important in the comparative genomics field since it should provide a combined view of data belonging to different genomes. We believe that existing tools are limited in this respect as they focus on a single genome at a time (conservation histograms) or compress alignment representation to a single dimension. We have therefore developed a web-based tool called Comparative Genome Viewer (Cgv): it integrates a bidimensional representation of alignments between two regions, both at small and big scales, with the richness of annotations present in other genome browsers. We give access to our system through a web-based interface that provides the user with an interactive representation that can be updated in real time using the mouse to move from region to region and to zoom in on interesting details.

  3. Comparative Genomics of Cryptosporidium

    Directory of Open Access Journals (Sweden)

    Aurélien J. Mazurie

    2013-01-01

    Full Text Available Until recently, the apicomplexan parasites, Cryptosporidium hominis and C. parvum, were considered the same species. However, the two parasites, now considered distinct species, exhibit significant differences in host range, infectivity, and pathogenicity, and their sequenced genomes exhibit only 95–97% identity. The availability of the complete genome sequences of these organisms provides the potential to identify the genetic variations that are responsible for the phenotypic differences between the two parasites. We compared the genome organization and structure, gene composition, the metabolic and other pathways, and the local sequence identity between the genes of these two Cryptosporidium species. Our observations show that the phenotypic differences between C. hominis and C. parvum are not due to gross genome rearrangements, structural alterations, gene deletions or insertions, metabolic capabilities, or other obvious genomic alterations. Rather, the results indicate that these genomes exhibit a remarkable structural and compositional conservation and suggest that the phenotypic differences observed are due to subtle variations in the sequences of proteins that act at the interface between the parasite and its host.

  4. Genomic Prediction from Whole Genome Sequence in Livestock: The 1000 Bull Genomes Project

    DEFF Research Database (Denmark)

    Hayes, Benjamin J; MacLeod, Iona M; Daetwyler, Hans D

    Advantages of using whole genome sequence data to predict genomic estimated breeding values (GEBV) include better persistence of accuracy of GEBV across generations and more accurate GEBV across breeds. The 1000 Bull Genomes Project provides a database of whole genome sequenced key ancestor bulls...

  5. A Review on Genomics APIs

    Directory of Open Access Journals (Sweden)

    Rajeswari Swaminathan

    2016-01-01

    Full Text Available The constant improvement and falling prices of whole human genome Next Generation Sequencing (NGS has resulted in rapid adoption of genomic information at both clinics and research institutions. Considered together, the complexity of genomics data, due to its large volume and diversity along with the need for genomic data sharing, has resulted in the creation of Application Programming Interface (API for secure, modular, interoperable access to genomic data from different applications, platforms, and even organizations. The Genomics APIs are a set of special protocols that assist software developers in dealing with multiple genomic data sources for building seamless, interoperable applications leading to the advancement of both genomic and clinical research. These APIs help define a standard for retrieval of genomic data from multiple sources as well as to better package genomic information for integration with Electronic Health Records. This review covers three currently available Genomics APIs: a Google Genomics, b SMART Genomics, and c 23andMe. The functionalities, reference implementations (if available and authentication protocols of each API are reviewed. A comparative analysis of the different features across the three APIs is provided in the Discussion section. Though Genomics APIs are still under active development and have yet to reach widespread adoption, they hold the promise to make building of complicated genomics applications easier with downstream constructive effects on healthcare.

  6. Genomes to Proteomes

    Energy Technology Data Exchange (ETDEWEB)

    Panisko, Ellen A. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Grigoriev, Igor [USDOE Joint Genome Inst., Walnut Creek, CA (United States); Daly, Don S. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Webb-Robertson, Bobbie-Jo [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Baker, Scott E. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

    2009-03-01

    Biologists are awash with genomic sequence data. In large part, this is due to the rapid acceleration in the generation of DNA sequence that occurred as public and private research institutes raced to sequence the human genome. In parallel with the large human genome effort, mostly smaller genomes of other important model organisms were sequenced. Projects following on these initial efforts have made use of technological advances and the DNA sequencing infrastructure that was built for the human and other organism genome projects. As a result, the genome sequences of many organisms are available in high quality draft form. While in many ways this is good news, there are limitations to the biological insights that can be gleaned from DNA sequences alone; genome sequences offer only a bird's eye view of the biological processes endemic to an organism or community. Fortunately, the genome sequences now being produced at such a high rate can serve as the foundation for other global experimental platforms such as proteomics. Proteomic methods offer a snapshot of the proteins present at a point in time for a given biological sample. Current global proteomics methods combine enzymatic digestion, separations, mass spectrometry and database searching for peptide identification. One key aspect of proteomics is the prediction of peptide sequences from mass spectrometry data. Global proteomic analysis uses computational matching of experimental mass spectra with predicted spectra based on databases of gene models that are often generated computationally. Thus, the quality of gene models predicted from a genome sequence is crucial in the generation of high quality peptide identifications. Once peptides are identified they can be assigned to their parent protein. Proteins identified as expressed in a given experiment are most useful when compared to other expressed proteins in a larger biological context or biochemical pathway. In this chapter we will discuss the automatic

  7. Genome Sequences of Oryza Species

    KAUST Repository

    Kumagai, Masahiko

    2018-02-14

    This chapter summarizes recent data obtained from genome sequencing, annotation projects, and studies on the genome diversity of Oryza sativa and related Oryza species. O. sativa, commonly known as Asian rice, is the first monocot species whose complete genome sequence was deciphered based on physical mapping by an international collaborative effort. This genome, along with its accurate and comprehensive annotation, has become an indispensable foundation for crop genomics and breeding. With the development of innovative sequencing technologies, genomic studies of O. sativa have dramatically increased; in particular, a large number of cultivars and wild accessions have been sequenced and compared with the reference rice genome. Since de novo genome sequencing has become cost-effective, the genome of African cultivated rice, O. glaberrima, has also been determined. Comparative genomic studies have highlighted the independent domestication processes of different rice species, but it also turned out that Asian and African rice share a common gene set that has experienced similar artificial selection. An international project aimed at constructing reference genomes and examining the genome diversity of wild Oryza species is currently underway, and the genomes of some species are publicly available. This project provides a platform for investigations such as the evolution, development, polyploidization, and improvement of crops. Studies on the genomic diversity of Oryza species, including wild species, should provide new insights to solve the problem of growing food demands in the face of rapid climatic changes.

  8. Genomics of Preterm Birth

    Science.gov (United States)

    Swaggart, Kayleigh A.; Pavlicev, Mihaela; Muglia, Louis J.

    2015-01-01

    The molecular mechanisms controlling human birth timing at term, or resulting in preterm birth, have been the focus of considerable investigation, but limited insights have been gained over the past 50 years. In part, these processes have remained elusive because of divergence in reproductive strategies and physiology shown by model organisms, making extrapolation to humans uncertain. Here, we summarize the evolution of progesterone signaling and variation in pregnancy maintenance and termination. We use this comparative physiology to support the hypothesis that selective pressure on genomic loci involved in the timing of parturition have shaped human birth timing, and that these loci can be identified with comparative genomic strategies. Previous limitations imposed by divergence of mechanisms provide an important new opportunity to elucidate fundamental pathways of parturition control through increasing availability of sequenced genomes and associated reproductive physiology characteristics across diverse organisms. PMID:25646385

  9. Genomics of Salmonella Species

    Science.gov (United States)

    Canals, Rocio; McClelland, Michael; Santiviago, Carlos A.; Andrews-Polymenis, Helene

    Progress in the study of Salmonella survival, colonization, and virulence has increased rapidly with the advent of complete genome sequencing and higher capacity assays for transcriptomic and proteomic analysis. Although many of these techniques have yet to be used to directly assay Salmonella growth on foods, these assays are currently in use to determine Salmonella factors necessary for growth in animal models including livestock animals and in in vitro conditions that mimic many different environments. As sequencing of the Salmonella genome and microarray analysis have revolutionized genomics and transcriptomics of salmonellae over the last decade, so are new high-throughput sequencing technologies currently accelerating the pace of our studies and allowing us to approach complex problems that were not previously experimentally tractable.

  10. Yeast genome sequencing:

    DEFF Research Database (Denmark)

    Piskur, Jure; Langkjær, Rikke Breinhold

    2004-01-01

    For decades, unicellular yeasts have been general models to help understand the eukaryotic cell and also our own biology. Recently, over a dozen yeast genomes have been sequenced, providing the basis to resolve several complex biological questions. Analysis of the novel sequence data has shown...... that the minimum number of genes from each species that need to be compared to produce a reliable phylogeny is about 20. Yeast has also become an attractive model to study speciation in eukaryotes, especially to understand molecular mechanisms behind the establishment of reproductive isolation. Comparison...... they are short and degenerate and occupy different positions. Comparative genomics helps to understand the origin of yeasts and points out crucial molecular events in yeast evolutionary history, such as whole-genome duplication and horizontal gene transfer(s). In addition, the accumulating sequence data provide...

  11. Genomics of Volvocine Algae

    Science.gov (United States)

    Umen, James G.; Olson, Bradley J.S.C.

    2015-01-01

    Volvocine algae are a group of chlorophytes that together comprise a unique model for evolutionary and developmental biology. The species Chlamydomonas reinhardtii and Volvox carteri represent extremes in morphological diversity within the Volvocine clade. Chlamydomonas is unicellular and reflects the ancestral state of the group, while Volvox is multicellular and has evolved numerous innovations including germ-soma differentiation, sexual dimorphism, and complex morphogenetic patterning. The Chlamydomonas genome sequence has shed light on several areas of eukaryotic cell biology, metabolism and evolution, while the Volvox genome sequence has enabled a comparison with Chlamydomonas that reveals some of the underlying changes that enabled its transition to multicellularity, but also underscores the subtlety of this transition. Many of the tools and resources are in place to further develop Volvocine algae as a model for evolutionary genomics. PMID:25883411

  12. Brief Guide to Genomics: DNA, Genes and Genomes

    Science.gov (United States)

    ... de genómica A Brief Guide to Genomics DNA, Genes and Genomes Deoxyribonucleic acid (DNA) is the chemical ... needed to build the entire human body. A gene traditionally refers to the unit of DNA that ...

  13. Methanococcus jannaschii genome: revisited

    Science.gov (United States)

    Kyrpides, N. C.; Olsen, G. J.; Klenk, H. P.; White, O.; Woese, C. R.

    1996-01-01

    Analysis of genomic sequences is necessarily an ongoing process. Initial gene assignments tend (wisely) to be on the conservative side (Venter, 1996). The analysis of the genome then grows in an iterative fashion as additional data and more sophisticated algorithms are brought to bear on the data. The present report is an emendation of the original gene list of Methanococcus jannaschii (Bult et al., 1996). By using a somewhat more updated database and more relaxed (and operator-intensive) pattern matching methods, we were able to add significantly to, and in a few cases amend, the gene identification table originally published by Bult et al. (1996).

  14. Comparative Genomics Reveals High Genomic Diversity in the Genus Photobacterium.

    Science.gov (United States)

    Machado, Henrique; Gram, Lone

    2017-01-01

    Vibrionaceae is a large marine bacterial family, which can constitute up to 50% of the prokaryotic population in marine waters. Photobacterium is the second largest genus in the family and we used comparative genomics on 35 strains representing 16 of the 28 species described so far, to understand the genomic diversity present in the Photobacterium genus. Such understanding is important for ecophysiology studies of the genus. We used whole genome sequences to evaluate phylogenetic relationships using several analyses (16S rRNA, MLSA, fur , amino-acid usage, ANI), which allowed us to identify two misidentified strains. Genome analyses also revealed occurrence of higher and lower GC content clades, correlating with phylogenetic clusters. Pan- and core-genome analysis revealed the conservation of 25% of the genome throughout the genus, with a large and open pan-genome. The major source of genomic diversity could be traced to the smaller chromosome and plasmids. Several of the physiological traits studied in the genus did not correlate with phylogenetic data. Since horizontal gene transfer (HGT) is often suggested as a source of genetic diversity and a potential driver of genomic evolution in bacterial species, we looked into evidence of such in Photobacterium genomes. Genomic islands were the source of genomic differences between strains of the same species. Also, we found transposase genes and CRISPR arrays that suggest multiple encounters with foreign DNA. Presence of genomic exchange traits was widespread and abundant in the genus, suggesting a role in genomic evolution. The high genetic variability and indications of genetic exchange make it difficult to elucidate genome evolutionary paths and raise the awareness of the roles of foreign DNA in the genomic evolution of environmental organisms.

  15. REBASE--a database for DNA restriction and modification: enzymes, genes and genomes.

    Science.gov (United States)

    Roberts, Richard J; Vincze, Tamas; Posfai, Janos; Macelis, Dana

    2015-01-01

    REBASE is a comprehensive and fully curated database of information about the components of restriction-modification (RM) systems. It contains fully referenced information about recognition and cleavage sites for both restriction enzymes and methyltransferases as well as commercial availability, methylation sensitivity, crystal and sequence data. All genomes that are completely sequenced are analyzed for RM system components, and with the advent of PacBio sequencing, the recognition sequences of DNA methyltransferases (MTases) are appearing rapidly. Thus, Type I and Type III systems can now be characterized in terms of recognition specificity merely by DNA sequencing. The contents of REBASE may be browsed from the web http://rebase.neb.com and selected compilations can be downloaded by FTP (ftp.neb.com). Monthly updates are also available via email. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  16. Incorporation of spatial interactions in location networks to identify critical geo-referenced routes for assessing disease control measures on a large-scale campus.

    Science.gov (United States)

    Wen, Tzai-Hung; Chin, Wei Chien Benny

    2015-04-14

    Respiratory diseases mainly spread through interpersonal contact. Class suspension is the most direct strategy to prevent the spread of disease through elementary or secondary schools by blocking the contact network. However, as university students usually attend courses in different buildings, the daily contact patterns on a university campus are complicated, and once disease clusters have occurred, suspending classes is far from an efficient strategy to control disease spread. The purpose of this study is to propose a methodological framework for generating campus location networks from a routine administration database, analyzing the community structure of the network, and identifying the critical links and nodes for blocking respiratory disease transmission. The data comes from the student enrollment records of a major comprehensive university in Taiwan. We combined the social network analysis and spatial interaction model to establish a geo-referenced community structure among the classroom buildings. We also identified the critical links among the communities that were acting as contact bridges and explored the changes in the location network after the sequential removal of the high-risk buildings. Instead of conducting a questionnaire survey, the study established a standard procedure for constructing a location network on a large-scale campus from a routine curriculum database. We also present how a location network structure at a campus could function to target the high-risk buildings as the bridges connecting communities for blocking disease transmission.

  17. Improving the Accuracy of Direct Geo-referencing of Smartphone-Based Mobile Mapping Systems Using Relative Orientation and Scene Geometric Constraints

    Directory of Open Access Journals (Sweden)

    Naif M. Alsubaie

    2017-09-01

    Full Text Available This paper introduces a new method which facilitate the use of smartphones as a handheld low-cost mobile mapping system (MMS. Smartphones are becoming more sophisticated and smarter and are quickly closing the gap between computers and portable tablet devices. The current generation of smartphones are equipped with low-cost GPS receivers, high-resolution digital cameras, and micro-electro mechanical systems (MEMS-based navigation sensors (e.g., accelerometers, gyroscopes, magnetic compasses, and barometers. These sensors are in fact the essential components for a MMS. However, smartphone navigation sensors suffer from the poor accuracy of global navigation satellite System (GNSS, accumulated drift, and high signal noise. These issues affect the accuracy of the initial Exterior Orientation Parameters (EOPs that are inputted into the bundle adjustment algorithm, which then produces inaccurate 3D mapping solutions. This paper proposes new methodologies for increasing the accuracy of direct geo-referencing of smartphones using relative orientation and smartphone motion sensor measurements as well as integrating geometric scene constraints into free network bundle adjustment. The new methodologies incorporate fusing the relative orientations of the captured images and their corresponding motion sensor measurements to improve the initial EOPs. Then, the geometric features (e.g., horizontal and vertical linear lines visible in each image are extracted and used as constraints in the bundle adjustment procedure which correct the relative position and orientation of the 3D mapping solution.

  18. Incorporation of Spatial Interactions in Location Networks to Identify Critical Geo-Referenced Routes for Assessing Disease Control Measures on a Large-Scale Campus

    Directory of Open Access Journals (Sweden)

    Tzai-Hung Wen

    2015-04-01

    Full Text Available Respiratory diseases mainly spread through interpersonal contact. Class suspension is the most direct strategy to prevent the spread of disease through elementary or secondary schools by blocking the contact network. However, as university students usually attend courses in different buildings, the daily contact patterns on a university campus are complicated, and once disease clusters have occurred, suspending classes is far from an efficient strategy to control disease spread. The purpose of this study is to propose a methodological framework for generating campus location networks from a routine administration database, analyzing the community structure of the network, and identifying the critical links and nodes for blocking respiratory disease transmission. The data comes from the student enrollment records of a major comprehensive university in Taiwan. We combined the social network analysis and spatial interaction model to establish a geo-referenced community structure among the classroom buildings. We also identified the critical links among the communities that were acting as contact bridges and explored the changes in the location network after the sequential removal of the high-risk buildings. Instead of conducting a questionnaire survey, the study established a standard procedure for constructing a location network on a large-scale campus from a routine curriculum database. We also present how a location network structure at a campus could function to target the high-risk buildings as the bridges connecting communities for blocking disease transmission.

  19. Illuminating the Druggable Genome (IDG)

    Data.gov (United States)

    Federal Laboratory Consortium — Results from the Human Genome Project revealed that the human genome contains 20,000 to 25,000 genes. A gene contains (encodes) the information that each cell uses...

  20. Chromatin dynamics in genome stability

    DEFF Research Database (Denmark)

    Nair, Nidhi; Shoaib, Muhammad; Sørensen, Claus Storgaard

    2017-01-01

    Genomic DNA is compacted into chromatin through packaging with histone and non-histone proteins. Importantly, DNA accessibility is dynamically regulated to ensure genome stability. This is exemplified in the response to DNA damage where chromatin relaxation near genomic lesions serves to promote ...... of chromatin structure regulation in maintaining genome integrity by multiple mechanisms including facilitating DNA repair and directly suppressing endogenous DNA damage.......Genomic DNA is compacted into chromatin through packaging with histone and non-histone proteins. Importantly, DNA accessibility is dynamically regulated to ensure genome stability. This is exemplified in the response to DNA damage where chromatin relaxation near genomic lesions serves to promote...... access of relevant enzymes to specific DNA regions for signaling and repair. Furthermore, recent data highlight genome maintenance roles of chromatin through the regulation of endogenous DNA-templated processes including transcription and replication. Here, we review research that shows the importance...

  1. The Nostoc punctiforme Genome

    Energy Technology Data Exchange (ETDEWEB)

    John C. Meeks

    2001-12-31

    Nostoc punctiforme is a filamentous cyanobacterium with extensive phenotypic characteristics and a relatively large genome, approaching 10 Mb. The phenotypic characteristics include a photoautotrophic, diazotrophic mode of growth, but N. punctiforme is also facultatively heterotrophic; its vegetative cells have multiple development alternatives, including terminal differentiation into nitrogen-fixing heterocysts and transient differentiation into spore-like akinetes or motile filaments called hormogonia; and N. punctiforme has broad symbiotic competence with fungi and terrestrial plants, including bryophytes, gymnosperms and an angiosperm. The shotgun-sequencing phase of the N. punctiforme strain ATCC 29133 genome has been completed by the Joint Genome Institute. Annotation of an 8.9 Mb database yielded 7432 open reading frames, 45% of which encode proteins with known or probable known function and 29% of which are unique to N. punctiforme. Comparative analysis of the sequence indicates a genome that is highly plastic and in a state of flux, with numerous insertion sequences and multilocus repeats, as well as genes encoding transposases and DNA modification enzymes. The sequence also reveals the presence of genes encoding putative proteins that collectively define almost all characteristics of cyanobacteria as a group. N. punctiforme has an extensive potential to sense and respond to environmental signals as reflected by the presence of more than 400 genes encoding sensor protein kinases, response regulators and other transcriptional factors. The signal transduction systems and any of the large number of unique genes may play essential roles in the cell differentiation and symbiotic interaction properties of N. punctiforme.

  2. RIKEN mouse genome encyclopedia.

    Science.gov (United States)

    Hayashizaki, Yoshihide

    2003-01-01

    We have been working to establish the comprehensive mouse full-length cDNA collection and sequence database to cover as many genes as we can, named Riken mouse genome encyclopedia. Recently we are constructing higher-level annotation (Functional ANnoTation Of Mouse cDNA; FANTOM) not only with homology search based annotation but also with expression data profile, mapping information and protein-protein database. More than 1,000,000 clones prepared from 163 tissues were end-sequenced to classify into 159,789 clusters and 60,770 representative clones were fully sequenced. As a conclusion, the 60,770 sequences contained 33,409 unique. The next generation of life science is clearly based on all of the genome information and resources. Based on our cDNA clones we developed the additional system to explore gene function. We developed cDNA microarray system to print all of these cDNA clones, protein-protein interaction screening system, protein-DNA interaction screening system and so on. The integrated database of all the information is very useful not only for analysis of gene transcriptional network and for the connection of gene to phenotype to facilitate positional candidate approach. In this talk, the prospect of the application of these genome resourced should be discussed. More information is available at the web page: http://genome.gsc.riken.go.jp/.

  3. Genomic prediction using subsampling.

    Science.gov (United States)

    Xavier, Alencar; Xu, Shizhong; Muir, William; Rainey, Katy Martin

    2017-03-24

    Genome-wide assisted selection is a critical tool for the genetic improvement of plants and animals. Whole-genome regression models in Bayesian framework represent the main family of prediction methods. Fitting such models with a large number of observations involves a prohibitive computational burden. We propose the use of subsampling bootstrap Markov chain in genomic prediction. Such method consists of fitting whole-genome regression models by subsampling observations in each round of a Markov Chain Monte Carlo. We evaluated the effect of subsampling bootstrap on prediction and computational parameters. Across datasets, we observed an optimal subsampling proportion of observations around 50% with replacement, and around 33% without replacement. Subsampling provided a substantial decrease in computation time, reducing the time to fit the model by half. On average, losses on predictive properties imposed by subsampling were negligible, usually below 1%. For each dataset, an optimal subsampling point that improves prediction properties was observed, but the improvements were also negligible. Combining subsampling with Gibbs sampling is an interesting ensemble algorithm. The investigation indicates that the subsampling bootstrap Markov chain algorithm substantially reduces computational burden associated with model fitting, and it may slightly enhance prediction properties.

  4. The Rhodobacter capsulatus genome

    Czech Academy of Sciences Publication Activity Database

    Haselkorn, R.; Lapidus, A.; Kogan, Y.; Vlček, Čestmír; Pačes, Jan; Pačes, Václav; Ulbrich, P.; Pečenková, Tamara; Rebrekov, D.; Milgram, A.; Mazur, M.; Cox, R.; Kyrpides, N.; Ivanova, N.; Kapatral, V.; Los, T.; Lykidis, A.; Mikhailova, N.; Reznik, G.; Vasieva, O.; Fonstein, M.

    2001-01-01

    Roč. 70, č. 1 (2001), s. 43-52 ISSN 0166-8595 R&D Projects: GA MŠk LN00A079 Institutional research plan: CEZ:AV0Z5052915 Keywords : genome * expression * gene Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 1.739, year: 2001

  5. Functional genomics of tomato

    Indian Academy of Sciences (India)

    2014-10-20

    Oct 20, 2014 ... very first challenge before scientists working on tomato functional biology is to exploit this high-quality reference sequence for tapping of the ... and exploitation of the genomic diversity present in Solanum genus, in general, and ..... associated with this tool retain its labour-intensive nature, ineffectiveness for ...

  6. Searching for genomic constraints

    International Nuclear Information System (INIS)

    Lio', P.; Ruffo, S.

    1998-01-01

    The authors have analyzed general properties of very long DNA sequences belonging to simple and complex organisms, by using different correlation methods. They have distinguished those base compositional rules that concern the entire genome which they call 'genomic constraints' from the rules that depend on the 'external natural selection' acting on single genes, i. e. protein-centered constraints. They show that G + C content, purine / pyrimidine distributions and biological complexity of the organism are the most important factors which determine base compositional rules and genome complexity. Three main facts are here reported: bacteria with high G + C content have more restrictions on base composition than those with low G + C content; at constant G + C content more complex organisms, ranging from prokaryotes to higher eukaryotes (e.g. human) display an increase of repeats 10-20 nucleotides long, which are also partly responsible for long-range correlations; work selection of length 3 to 10 is stronger in human and in bacteria for two distinct reasons. With respect to previous studies, they have also compared the genomic sequence of the archeon Methanococcus jannaschii with those of bacteria and eukaryotes: it shows sometimes an intermediate statistical behaviour

  7. Better chocolate through genomics

    Science.gov (United States)

    Theobroma cacao, the cacao or chocolate tree, is a tropical understory tree whose seeds are used to make chocolate. And like any important crop, cacao is the subject of much research. On September 15, 2010, scientists publicly released a preliminary sequence of the cacao genome--which contains all o...

  8. Genomics of human longevity

    NARCIS (Netherlands)

    Slagboom, P. E.; Beekman, M.; Passtoors, W. M.; Deelen, J.; Vaarhorst, A. A.M.; Boer, J. M.; Van Den Akker, E. B.; Van Heemst, D.; De Craen, A. J.M.; Maier, A. B.; Rozing, M.; Mooijaart, S. P.; Heijmans, B. T.; Westendorp, R. G.J.

    2011-01-01

    In animal models, single-gene mutations in genes involved in insulin/IGF and target of rapamycin signalling pathways extend lifespan to a considerable extent. The genetic, genomic and epigenetic influences on human longevity are expected to be much more complex. Strikingly however, beneficial

  9. Genome stability in Caenorhabditis elegans

    NARCIS (Netherlands)

    Haaften, G.W. van

    2006-01-01

    Genome stability is closely linked to cancer. Most, if not all tumor cells show some form of genome instability, mutations can range from single point mutations to gross chromosomal rearrangements and aneuploidy. Genome instability is believed to be the driving force behind tumorigenesis. In order

  10. GenomeGraphs: integrated genomic data visualization with R

    Directory of Open Access Journals (Sweden)

    Spellman Paul T

    2009-01-01

    Full Text Available Abstract Background Biological studies involve a growing number of distinct high-throughput experiments to characterize samples of interest. There is a lack of methods to visualize these different genomic datasets in a versatile manner. In addition, genomic data analysis requires integrated visualization of experimental data along with constantly changing genomic annotation and statistical analyses. Results We developed GenomeGraphs, as an add-on software package for the statistical programming environment R, to facilitate integrated visualization of genomic datasets. GenomeGraphs uses the biomaRt package to perform on-line annotation queries to Ensembl and translates these to gene/transcript structures in viewports of the grid graphics package. This allows genomic annotation to be plotted together with experimental data. GenomeGraphs can also be used to plot custom annotation tracks in combination with different experimental data types together in one plot using the same genomic coordinate system. Conclusion GenomeGraphs is a flexible and extensible software package which can be used to visualize a multitude of genomic datasets within the statistical programming environment R.

  11. GenomeGraphs: integrated genomic data visualization with R.

    Science.gov (United States)

    Durinck, Steffen; Bullard, James; Spellman, Paul T; Dudoit, Sandrine

    2009-01-06

    Biological studies involve a growing number of distinct high-throughput experiments to characterize samples of interest. There is a lack of methods to visualize these different genomic datasets in a versatile manner. In addition, genomic data analysis requires integrated visualization of experimental data along with constantly changing genomic annotation and statistical analyses. We developed GenomeGraphs, as an add-on software package for the statistical programming environment R, to facilitate integrated visualization of genomic datasets. GenomeGraphs uses the biomaRt package to perform on-line annotation queries to Ensembl and translates these to gene/transcript structures in viewports of the grid graphics package. This allows genomic annotation to be plotted together with experimental data. GenomeGraphs can also be used to plot custom annotation tracks in combination with different experimental data types together in one plot using the same genomic coordinate system. GenomeGraphs is a flexible and extensible software package which can be used to visualize a multitude of genomic datasets within the statistical programming environment R.

  12. Implementing genomics and pharmacogenomics in the clinic: The National Human Genome Research Institute's genomic medicine portfolio.

    Science.gov (United States)

    Manolio, Teri A

    2016-10-01

    Increasing knowledge about the influence of genetic variation on human health and growing availability of reliable, cost-effective genetic testing have spurred the implementation of genomic medicine in the clinic. As defined by the National Human Genome Research Institute (NHGRI), genomic medicine uses an individual's genetic information in his or her clinical care, and has begun to be applied effectively in areas such as cancer genomics, pharmacogenomics, and rare and undiagnosed diseases. In 2011 NHGRI published its strategic vision for the future of genomic research, including an ambitious research agenda to facilitate and promote the implementation of genomic medicine. To realize this agenda, NHGRI is consulting and facilitating collaborations with the external research community through a series of "Genomic Medicine Meetings," under the guidance and leadership of the National Advisory Council on Human Genome Research. These meetings have identified and begun to address significant obstacles to implementation, such as lack of evidence of efficacy, limited availability of genomics expertise and testing, lack of standards, and difficulties in integrating genomic results into electronic medical records. The six research and dissemination initiatives comprising NHGRI's genomic research portfolio are designed to speed the evaluation and incorporation, where appropriate, of genomic technologies and findings into routine clinical care. Actual adoption of successful approaches in clinical care will depend upon the willingness, interest, and energy of professional societies, practitioners, patients, and payers to promote their responsible use and share their experiences in doing so. Published by Elsevier Ireland Ltd.

  13. Genome Editing Tools in Plants

    Directory of Open Access Journals (Sweden)

    Tapan Kumar Mohanta

    2017-12-01

    Full Text Available Genome editing tools have the potential to change the genomic architecture of a genome at precise locations, with desired accuracy. These tools have been efficiently used for trait discovery and for the generation of plants with high crop yields and resistance to biotic and abiotic stresses. Due to complex genomic architecture, it is challenging to edit all of the genes/genomes using a particular genome editing tool. Therefore, to overcome this challenging task, several genome editing tools have been developed to facilitate efficient genome editing. Some of the major genome editing tools used to edit plant genomes are: Homologous recombination (HR, zinc finger nucleases (ZFNs, transcription activator-like effector nucleases (TALENs, pentatricopeptide repeat proteins (PPRs, the CRISPR/Cas9 system, RNA interference (RNAi, cisgenesis, and intragenesis. In addition, site-directed sequence editing and oligonucleotide-directed mutagenesis have the potential to edit the genome at the single-nucleotide level. Recently, adenine base editors (ABEs have been developed to mutate A-T base pairs to G-C base pairs. ABEs use deoxyadeninedeaminase (TadA with catalytically impaired Cas9 nickase to mutate A-T base pairs to G-C base pairs.

  14. Evolution of small prokaryotic genomes

    Directory of Open Access Journals (Sweden)

    David José Martínez-Cano

    2015-01-01

    Full Text Available As revealed by genome sequencing, the biology of prokaryotes with reduced genomes is strikingly diverse. These include free-living prokaryotes with ~800 genes as well as endosymbiotic bacteria with as few as ~140 genes. Comparative genomics is revealing the evolutionary mechanisms that led to these small genomes. In the case of free-living prokaryotes, natural selection directly favored genome reduction, while in the case of endosymbiotic prokaryotes neutral processes played a more prominent role. However, new experimental data suggest that selective processes may be at operation as well for endosymbiotic prokaryotes at least during the first stages of genome reduction. Endosymbiotic prokaryotes have evolved diverse strategies for living with reduced gene sets inside a host-defined medium. These include utilization of host-encoded functions (some of them coded by genes acquired by gene transfer from the endosymbiont and/or other bacteria; metabolic complementation between co-symbionts; and forming consortiums with other bacteria within the host. Recent genome sequencing projects of intracellular mutualistic bacteria showed that previously believed universal evolutionary trends like reduced G+C content and conservation of genome synteny are not always present in highly reduced genomes. Finally, the simplified molecular machinery of some of these organisms with small genomes may be used to aid in the design of artificial minimal cells. Here we review recent genomic discoveries of the biology of prokaryotes endowed with small gene sets and discuss the evolutionary mechanisms that have been proposed to explain their peculiar nature.

  15. Toward genome-enabled mycology.

    Science.gov (United States)

    Hibbett, David S; Stajich, Jason E; Spatafora, Joseph W

    2013-01-01

    Genome-enabled mycology is a rapidly expanding field that is characterized by the pervasive use of genome-scale data and associated computational tools in all aspects of fungal biology. Genome-enabled mycology is integrative and often requires teams of researchers with diverse skills in organismal mycology, bioinformatics and molecular biology. This issue of Mycologia presents the first complete fungal genomes in the history of the journal, reflecting the ongoing transformation of mycology into a genome-enabled science. Here, we consider the prospects for genome-enabled mycology and the technical and social challenges that will need to be overcome to grow the database of complete fungal genomes and enable all fungal biologists to make use of the new data.

  16. Marine Bacterial Genomics

    DEFF Research Database (Denmark)

    Machado, Henrique

    microorganisms to be used as cell factories for production. Therefore exploitation of new microbial niches and use of different strategies is an opportunity to boost discoveries. Even though scientists have started to explore several habitats other than the terrestrial ones, the marine environment stands out...... as a hitherto under-explored niche. This thesis work uses high-throughput sequencing technologies on a collection of marine bacteria established during the Galathea 3 expedition, with the purpose of unraveling new biodiversity and new bioactivities. Several tools were used for genomic analysis in order...... to better understand the potential harbored in marine bacteria. The work presented makes use of whole genome sequencing of marine bacteria to prove that the genetic repertoire for secondary metabolite production harbored in these bacteria is far larger than anticipated; to identify and develop a new...

  17. Genomic dairy cattle breeding

    DEFF Research Database (Denmark)

    Mark, Thomas; Sandøe, Peter

    2010-01-01

    , unfavourable genetic trends for metabolic, reproductive, claw and leg diseases indicate that these attempts have been insufficient. Today, novel genome-wide sequencing techniques are revolutionising dairy cattle breeding; these enable genetic changes to occur at least twice as rapidly as previously. While......, a number of potential risks are discussed, including detrimental genetic trends for non-measured welfare traits, the increased chance of spreading unfavourable mutations, reduced sharing of information arising from concerns over patents, and an increased monopoly within dairy cattle breeding that may make...... negative effects on animal welfare and to invest in breeding for increased animal welfare. Researchers are encouraged to further investigate the long-term effects of various breeding schemes that rely on genomic breeding values....

  18. Precision genome editing

    DEFF Research Database (Denmark)

    Steentoft, Catharina; Bennett, Eric P; Schjoldager, Katrine Ter-Borch Gram

    2014-01-01

    of glycobiology, primarily due to their low efficiencies, with resultant failure to impose substantial phenotypic consequences upon the final glycosylation products. Here, we review novel nuclease-based precision genome editing techniques enabling efficient and stable gene editing, including gene disruption......Precise and stable gene editing in mammalian cell lines has until recently been hampered by the lack of efficient targeting methods. While different gene silencing strategies have had tremendous impact on many biological fields, they have generally not been applied with wide success in the field...... by introducing single or double-stranded breaks at a defined genomic sequence. We here compare and contrast the different techniques and summarize their current applications, highlighting cases from the field of glycobiology as well as pointing to future opportunities. The emerging potential of precision gene...

  19. Genomic research perspectives in Kazakhstan

    Directory of Open Access Journals (Sweden)

    Ainur Akilzhanova

    2014-01-01

    Full Text Available Introduction: Technological advancements rapidly propel the field of genome research. Advances in genetics and genomics such as the sequence of the human genome, the human haplotype map, open access databases, cheaper genotyping and chemical genomics, have transformed basic and translational biomedical research. Several projects in the field of genomic and personalized medicine have been conducted at the Center for Life Sciences in Nazarbayev University. The prioritized areas of research include: genomics of multifactorial diseases, cancer genomics, bioinformatics, genetics of infectious diseases and population genomics. At present, DNA-based risk assessment for common complex diseases, application of molecular signatures for cancer diagnosis and prognosis, genome-guided therapy, and dose selection of therapeutic drugs are the important issues in personalized medicine. Results: To further develop genomic and biomedical projects at Center for Life Sciences, the development of bioinformatics research and infrastructure and the establishment of new collaborations in the field are essential. Widespread use of genetic tools will allow the identification of diseases before the onset of clinical symptoms, the individualization of drug treatment, and could induce individual behavioral changes on the basis of calculated disease risk. However, many challenges remain for the successful translation of genomic knowledge and technologies into health advances, such as medicines and diagnostics. It is important to integrate research and education in the fields of genomics, personalized medicine, and bioinformatics, which will be possible with opening of the new Medical Faculty at Nazarbayev University. People in practice and training need to be educated about the key concepts of genomics and engaged so they can effectively apply their knowledge in a matter that will bring the era of genomic medicine to patient care. This requires the development of well

  20. Phase referencing in optical interferometry

    OpenAIRE

    Filho, Mercedes E; Garcia, Paulo; Duvert, Gilles; Duchene, Gaspard; Thiebaut, Eric; Young, John; Absil, Olivier; Berger, Jean-Phillipe; Beckert, Thomas; Hoenig, Sebastian; Schertl, Dieter; Weigelt, Gerd; Testi, Leonardo; Tatuli, Eric; Borkowski, Virginie

    2008-01-01

    One of the aims of next generation optical interferometric instrumentation is to be able to make use of information contained in the visibility phase to construct high dynamic range images. Radio and optical interferometry are at the two extremes of phase corruption by the atmosphere. While in radio it is possible to obtain calibrated phases for the science objects, in the optical this is currently not possible. Instead, optical interferometry has relied on closure phase techniques to produce...

  1. Genomics Portals: integrative web-platform for mining genomics data.

    Science.gov (United States)

    Shinde, Kaustubh; Phatak, Mukta; Johannes, Freudenberg M; Chen, Jing; Li, Qian; Vineet, Joshi K; Hu, Zhen; Ghosh, Krishnendu; Meller, Jaroslaw; Medvedovic, Mario

    2010-01-13

    A large amount of experimental data generated by modern high-throughput technologies is available through various public repositories. Our knowledge about molecular interaction networks, functional biological pathways and transcriptional regulatory modules is rapidly expanding, and is being organized in lists of functionally related genes. Jointly, these two sources of information hold a tremendous potential for gaining new insights into functioning of living systems. Genomics Portals platform integrates access to an extensive knowledge base and a large database of human, mouse, and rat genomics data with basic analytical visualization tools. It provides the context for analyzing and interpreting new experimental data and the tool for effective mining of a large number of publicly available genomics datasets stored in the back-end databases. The uniqueness of this platform lies in the volume and the diversity of genomics data that can be accessed and analyzed (gene expression, ChIP-chip, ChIP-seq, epigenomics, computationally predicted binding sites, etc), and the integration with an extensive knowledge base that can be used in such analysis. The integrated access to primary genomics data, functional knowledge and analytical tools makes Genomics Portals platform a unique tool for interpreting results of new genomics experiments and for mining the vast amount of data stored in the Genomics Portals backend databases. Genomics Portals can be accessed and used freely at http://GenomicsPortals.org.

  2. eGenomics: Cataloguing Our Complete Genome Collection III

    Directory of Open Access Journals (Sweden)

    Dawn Field

    2007-01-01

    Full Text Available This meeting report summarizes the proceedings of the “eGenomics: Cataloguing our Complete Genome Collection III” workshop held September 11–13, 2006, at the National Institute for Environmental eScience (NIEeS, Cambridge, United Kingdom. This 3rd workshop of the Genomic Standards Consortium was divided into two parts. The first half of the three-day workshop was dedicated to reviewing the genomic diversity of our current and future genome and metagenome collection, and exploring linkages to a series of existing projects through formal presentations. The second half was dedicated to strategic discussions. Outcomes of the workshop include a revised “Minimum Information about a Genome Sequence” (MIGS specification (v1.1, consensus on a variety of features to be added to the Genome Catalogue (GCat, agreement by several researchers to adopt MIGS for imminent genome publications, and an agreement by the EBI and NCBI to input their genome collections into GCat for the purpose of quantifying the amount of optional data already available (e.g., for geographic location coordinates and working towards a single, global list of all public genomes and metagenomes.

  3. Genomics Portals: integrative web-platform for mining genomics data

    Science.gov (United States)

    2010-01-01

    Background A large amount of experimental data generated by modern high-throughput technologies is available through various public repositories. Our knowledge about molecular interaction networks, functional biological pathways and transcriptional regulatory modules is rapidly expanding, and is being organized in lists of functionally related genes. Jointly, these two sources of information hold a tremendous potential for gaining new insights into functioning of living systems. Results Genomics Portals platform integrates access to an extensive knowledge base and a large database of human, mouse, and rat genomics data with basic analytical visualization tools. It provides the context for analyzing and interpreting new experimental data and the tool for effective mining of a large number of publicly available genomics datasets stored in the back-end databases. The uniqueness of this platform lies in the volume and the diversity of genomics data that can be accessed and analyzed (gene expression, ChIP-chip, ChIP-seq, epigenomics, computationally predicted binding sites, etc), and the integration with an extensive knowledge base that can be used in such analysis. Conclusion The integrated access to primary genomics data, functional knowledge and analytical tools makes Genomics Portals platform a unique tool for interpreting results of new genomics experiments and for mining the vast amount of data stored in the Genomics Portals backend databases. Genomics Portals can be accessed and used freely at http://GenomicsPortals.org. PMID:20070909

  4. Population-referenced percentiles for waist-worn accelerometer-derived total activity counts in U.S. youth: 2003 - 2006 NHANES.

    Directory of Open Access Journals (Sweden)

    Dana L Wolff-Hughes

    Full Text Available The total activity volume performed is an overall measure that takes into account the frequency, intensity, and duration of activities performed. The importance of considering total activity volume is shown by recent studies indicating that light physical activity (LPA and intermittent moderate-to-vigorous physical activity (MVPA have health benefits. Accelerometer-derived total activity counts (TAC per day from a waist-worn accelerometer can serve as a proxy for an individual's total activity volume. The purpose of this study was to develop age- and gender-specific percentiles for daily TAC, minutes of MVPA, and minutes of LPA in U.S. youth ages 6 - 19 y.Data from the 2003 - 2006 NHANES waist-worn accelerometer component were used in this analysis. The sample was composed of youth aged 6 - 19 years with at least 4 d of ≥ 10 hours of accelerometer wear time (N = 3698. MVPA was defined using age specific cutpoints as the total number of minutes at ≥4 metabolic equivalents (METs for youth 6 - 17 y or minutes with ≥2020 counts for youth 18 - 19 y. LPA was defined as the total number of minutes between 100 counts and the MVPA threshold. TAC/d, MVPA, and LPA were averaged across all valid days.For males in the 50th percentile, the median activity level was 441,431 TAC/d, with 53 min/d of MVPA and 368 min/d of LPA. The median level of activity for females was 234,322 TAC/d, with 32 min/d of MVPA and 355 min/d of LPA.Population referenced TAC/d percentiles for U.S. youth ages 6-19 y provide a novel means of characterizing the total activity volume performed by children and adolescents.

  5. Simulating stream transport of nutrients in the eastern United States, 2002, using a spatially-referenced regression model and 1:100,000-scale hydrography

    Science.gov (United States)

    Hoos, Anne B.; Moore, Richard B.; Garcia, Ana Maria; Noe, Gregory B.; Terziotti, Silvia E.; Johnston, Craig M.; Dennis, Robin L.

    2013-01-01

    Existing Spatially Referenced Regression on Watershed attributes (SPARROW) nutrient models for the northeastern and southeastern regions of the United States were recalibrated to achieve a hydrographically consistent model with which to assess nutrient sources and stream transport and investigate specific management questions about the effects of wetlands and atmospheric deposition on nutrient transport. Recalibrated nitrogen models for the northeast and southeast were sufficiently similar to be merged into a single nitrogen model for the eastern United States. The atmospheric deposition source in the nitrogen model has been improved to account for individual components of atmospheric input, derived from emissions from agricultural manure, agricultural livestock, vehicles, power plants, other industry, and background sources. This accounting makes it possible to simulate the effects of altering an individual component of atmospheric deposition, such as nitrate emissions from vehicles or power plants. Regional differences in transport of phosphorus through wetlands and reservoirs were investigated and resulted in two distinct phosphorus models for the northeast and southeast. The recalibrated nitrogen and phosphorus models account explicitly for the influence of wetlands on regional-scale land-phase and aqueous-phase transport of nutrients and therefore allow comparison of the water-quality functions of different wetland systems over large spatial scales. Seven wetland systems were associated with enhanced transport of either nitrogen or phosphorus in streams, probably because of the export of dissolved organic nitrogen and bank erosion. Six wetland systems were associated with mitigating the delivery of either nitrogen or phosphorus to streams, probably because of sedimentation, phosphate sorption, and ground water infiltration.

  6. The Genome Atlas Resource

    DEFF Research Database (Denmark)

    Azam Qureshi, Matloob; Rotenberg, Eva; Stærfeldt, Hans Henrik

    2010-01-01

    with scripts and algorithms developed in a variety of programming languages at the Centre for Biological Sequence Analysis in order to create a three-tier software application for genome analysis. The results are made available via a web interface developed in Java, PHP and Perl CGI. User......-configurable and dynamic views of Chromosomal maps are made possible through an updated GeneWiz browser (version 0.94) which uses Java to allow rapid zooming in and out of the atlases....

  7. Malaria Genome Sequencing Project

    Science.gov (United States)

    2004-01-01

    proteins in plastid segregation mutants of Toxoplasma gandii. L. Biot. Parasito . Today 11, 1-4 (1995). Chem. 276, 28436-28442 (2001). 11. Su, X. et al... parasito - gene mapping studies have shown that regions of gene synteny exist phorous vacuole membrane29 . between species of rodent malaria9 and between...Carucci, D. J. Rodent models of malaria in the genomics era. Trends Parasito , 18, selection of karyotype mutants and non-gametocyte producer mutants

  8. National Plant Genome Initiative

    Science.gov (United States)

    2004-01-01

    from the soil allow the development of new strategies for fortification of plant foods with nutrients beneficial to human and animal health ( iron and... calcium , for example) and might suggest new approaches for using plants to clean up soils with unsafe levels of heavy metal pollutants such as...involved in uptake of iron , a key nutrient for human health, thus validating the approach. Based upon past studies of genomic and EST sequences, it was

  9. Human Germline Genome Editing.

    Science.gov (United States)

    Ormond, Kelly E; Mortlock, Douglas P; Scholes, Derek T; Bombard, Yvonne; Brody, Lawrence C; Faucett, W Andrew; Garrison, Nanibaa' A; Hercher, Laura; Isasi, Rosario; Middleton, Anna; Musunuru, Kiran; Shriner, Daniel; Virani, Alice; Young, Caroline E

    2017-08-03

    With CRISPR/Cas9 and other genome-editing technologies, successful somatic and germline genome editing are becoming feasible. To respond, an American Society of Human Genetics (ASHG) workgroup developed this position statement, which was approved by the ASHG Board in March 2017. The workgroup included representatives from the UK Association of Genetic Nurses and Counsellors, Canadian Association of Genetic Counsellors, International Genetic Epidemiology Society, and US National Society of Genetic Counselors. These groups, as well as the American Society for Reproductive Medicine, Asia Pacific Society of Human Genetics, British Society for Genetic Medicine, Human Genetics Society of Australasia, Professional Society of Genetic Counselors in Asia, and Southern African Society for Human Genetics, endorsed the final statement. The statement includes the following positions. (1) At this time, given the nature and number of unanswered scientific, ethical, and policy questions, it is inappropriate to perform germline gene editing that culminates in human pregnancy. (2) Currently, there is no reason to prohibit in vitro germline genome editing on human embryos and gametes, with appropriate oversight and consent from donors, to facilitate research on the possible future clinical applications of gene editing. There should be no prohibition on making public funds available to support this research. (3) Future clinical application of human germline genome editing should not proceed unless, at a minimum, there is (a) a compelling medical rationale, (b) an evidence base that supports its clinical use, (c) an ethical justification, and (d) a transparent public process to solicit and incorporate stakeholder input. Copyright © 2017 American Society of Human Genetics. All rights reserved.

  10. Genomic technologies in neonatology

    Directory of Open Access Journals (Sweden)

    L. N. Chernova

    2017-01-01

    Full Text Available In recent years, there has been a tremendous trend toward personalized medicine. Advances in the field forced clinicians, including neonatologists, to take a fresh look at prevention, tactics of management and therapy of various diseases. In the center of attention of foreign, and increasingly Russian, researchers and doctors, there are individual genomic data that allow not only to assess the risks of some form of pathology, but also to successfully apply personalized strategies of prediction, prevention and targeted treatment. This article provides a brief review of the latest achievements of genomic technologies in newborns, examines the problems and potential applications of genomics in promoting the concept of personalized medicine in neonatology. The increasing amount of personalized data simply impossible to analyze only by the human mind. In this connection, the need of computers and bioinformatics is obvious. The article reveals the role of translational bioinformatics in the analysis and integration of the results of the accumulated fundamental research into complete clinical decisions. The latest advances in neonatal translational bioinformatics such as clinical decision support systems are considered. It helps to monitor vital parameters of newborns influencing the course of a particular disease, to calculate the increased risks of the development of various pathologies and to select the drugs.

  11. Nutritional genomics: an approach to the genome-environment interaction

    OpenAIRE

    Xacur-Garcia, F.; Castillo-Quan, J. I.; Hernandez-Escalante, V. M.; Laviada-Molina, H.

    2008-01-01

    Nutritional genomics forms part of the genomic sciences and addresses the interaction between genes and the human diet, its influence on metabolism and subsequent susceptibility to develop common diseases. It encompasses both nutrigenomics, which explores the effects of nutrients on the genome, proteome and metabolome; and nutrigenetics, that explores the effects of genetic variations on the diet/disease interaction. A number of mechanisms drive the gene/diet interaction: elements in the diet...

  12. Genomic Data Commons and Genomic Cloud Pilots - Google Hangout

    Science.gov (United States)

    Join us for a live, moderated discussion about two NCI efforts to expand access to cancer genomics data: the Genomic Data Commons and Genomic Cloud Pilots. NCI subject matters experts will include Louis M. Staudt, M.D., Ph.D., Director Center for Cancer Genomics, Warren Kibbe, Ph.D., Director, NCI Center for Biomedical Informatics and Information Technology, and moderated by Anthony Kerlavage, Ph.D., Chief, Cancer Informatics Branch, Center for Biomedical Informatics and Information Technology. We welcome your questions before and during the Hangout on Twitter using the hashtag #AskNCI.

  13. Invariants of DNA genomic signals

    Science.gov (United States)

    Cristea, Paul Dan A.

    2005-02-01

    For large scale analysis purposes, the conversion of genomic sequences into digital signals opens the possibility to use powerful signal processing methods for handling genomic information. The study of complex genomic signals reveals large scale features, maintained over the scale of whole chromosomes, that would be difficult to find by using only the symbolic representation. Based on genomic signal methods and on statistical techniques, the paper defines parameters of DNA sequences which are invariant to transformations induced by SNPs, splicing or crossover. Re-orienting concatenated coding regions in the same direction, regularities shared by the genomic material in all exons are revealed, pointing towards the hypothesis of a regular ancestral structure from which the current chromosome structures have evolved. This property is not found in non-nuclear genomic material, e.g., plasmids.

  14. Comparative Genomics in Homo sapiens.

    Science.gov (United States)

    Oti, Martin; Sammeth, Michael

    2018-01-01

    Genomes can be compared at different levels of divergence, either between species or within species. Within species genomes can be compared between different subpopulations, such as human subpopulations from different continents. Investigating the genomic differences between different human subpopulations is important when studying complex diseases that are affected by many genetic variants, as the variants involved can differ between populations. The 1000 Genomes Project collected genome-scale variation data for 2504 human individuals from 26 different populations, enabling a systematic comparison of variation between human subpopulations. In this chapter, we present step-by-step a basic protocol for the identification of population-specific variants employing the 1000 Genomes data. These variants are subsequently further investigated for those that affect the proteome or RNA splice sites, to investigate potentially biologically relevant differences between the populations.

  15. Genomic selection in plant breeding.

    Science.gov (United States)

    Newell, Mark A; Jannink, Jean-Luc

    2014-01-01

    Genomic selection (GS) is a method to predict the genetic value of selection candidates based on the genomic estimated breeding value (GEBV) predicted from high-density markers positioned throughout the genome. Unlike marker-assisted selection, the GEBV is based on all markers including both minor and major marker effects. Thus, the GEBV may capture more of the genetic variation for the particular trait under selection.

  16. Advances in editing microalgae genomes

    OpenAIRE

    Daboussi, Fayza

    2017-01-01

    There have been significant advances in microalgal genomics over the last decade. Nevertheless, there are still insufficient tools for the manipulation of microalgae genomes and the development of microalgae as industrial biofactories. Several research groups have recently contributed to progress by demonstrating that particular nucleases can be used for targeted and stable modifications of the genomes of some microalgae species. The nucleases include Meganucleases, Zinc Finger nucleases, TAL...

  17. Comparative RNA genomics

    DEFF Research Database (Denmark)

    Backofen, Rolf; Gorodkin, Jan; Hofacker, Ivo L.

    2018-01-01

    small RNAs is their reliance of conserved secondary structures. Large scale sequencing projects, on the other hand, have profoundly changed our understanding of eukaryotic genomes. Pervasively transcribed, they give rise to a plethora of large and evolutionarily extremely flexible noncoding RNAs...... that exert a vastly diverse array of molecule functions. In this chapter we provide a—necessarily incomplete—overview of the current state of comparative analysis of noncoding RNAs, emphasizing computational approaches as a means to gain a global picture of the modern RNA world....

  18. Genomic rearrangements and diseases

    OpenAIRE

    Loviglio, M. N.

    2016-01-01

    Copy number variations (CNVs) are major contributors of genomic imbalances disorders. On the short arm of chromosome 16, CNVs of the distal 220 kb BP2-BP3 region show mirror effect on BMI and head size, and association with autism and schizophrenia, as previously reported for the proximal 600 kb BP4-BP5 deletion and duplication. These two CNVs-prone regions at 16p11.2 are also reciprocally engaged in complex chromatin looping, successfully confirmed by 4C-seq, FISH, Hi-C and concomitant...

  19. Genomic taxonomy of vibrios

    DEFF Research Database (Denmark)

    Thompson, Cristiane C.; Vicente, Ana Carolina P.; Souza, Rangel C.

    2009-01-01

    BACKGROUND: Vibrio taxonomy has been based on a polyphasic approach. In this study, we retrieve useful taxonomic information (i.e. data that can be used to distinguish different taxonomic levels, such as species and genera) from 32 genome sequences of different vibrio species. We use a variety...... > 95% DNA identity in MLSA and supertree analysis, > 96% AAI, 61% proteome identity. Strains of the same species and species of the same genus will form monophyletic groups on the basis of MLSA and supertree. CONCLUSION: The combination of different......-based server. This novel approach to microbial systematics will result in a tremendous advance concerning biodiversity discovery, description, and understanding....

  20. Genomic effects of glucocorticoids.

    Science.gov (United States)

    Grbesa, Ivana; Hakim, Ofir

    2017-05-01

    Glucocorticoids and their receptor (GR) have been an important area of research because of their pleiotropic physiological functions and extensive use in the clinic. In addition, the association between GR and glucocorticoids, which is highly specific, leads to rapid nuclear translocation where GR associates with chromatin to regulate gene transcription. This simplified model system has been instrumental for studying the complexity of transcription regulation processes occurring at chromatin. In this review we discuss our current understanding of GR action that has been enhanced by recent developments in genome wide measurements of chromatin accessibility, histone marks, chromatin remodeling and 3D chromatin structure in various cell types responding to glucocorticoids.

  1. Genomic Feature Models

    DEFF Research Database (Denmark)

    Sørensen, Peter; Edwards, Stefan McKinnon; Rohde, Palle Duun

    -additive genetic mechanisms. These modeling approaches have proven to be highly useful to determine population genetic parameters as well as prediction of genetic risk or value. We present a series of statistical modelling approaches that use prior biological information for evaluating the collective action......Whole-genome sequences and multiple trait phenotypes from large numbers of individuals will soon be available in many populations. Well established statistical modeling approaches enable the genetic analyses of complex trait phenotypes while accounting for a variety of additive and non...

  2. Organizational heterogeneity of vertebrate genomes.

    Directory of Open Access Journals (Sweden)

    Svetlana Frenkel

    Full Text Available Genomes of higher eukaryotes are mosaics of segments with various structural, functional, and evolutionary properties. The availability of whole-genome sequences allows the investigation of their structure as "texts" using different statistical and computational methods. One such method, referred to as Compositional Spectra (CS analysis, is based on scoring the occurrences of fixed-length oligonucleotides (k-mers in the target DNA sequence. CS analysis allows generating species- or region-specific characteristics of the genome, regardless of their length and the presence of coding DNA. In this study, we consider the heterogeneity of vertebrate genomes as a joint effect of regional variation in sequence organization superimposed on the differences in nucleotide composition. We estimated compositional and organizational heterogeneity of genome and chromosome sequences separately and found that both heterogeneity types vary widely among genomes as well as among chromosomes in all investigated taxonomic groups. The high correspondence of heterogeneity scores obtained on three genome fractions, coding, repetitive, and the remaining part of the noncoding DNA (the genome dark matter--GDM allows the assumption that CS-heterogeneity may have functional relevance to genome regulation. Of special interest for such interpretation is the fact that natural GDM sequences display the highest deviation from the corresponding reshuffled sequences.

  3. Genome Trees from Conservation Profiles.

    Directory of Open Access Journals (Sweden)

    2005-12-01

    Full Text Available The concept of the genome tree depends on the potential evolutionary significance in the clustering of species according to similarities in the gene content of their genomes. In this respect, genome trees have often been identified with species trees. With the rapid expansion of genome sequence data it becomes of increasing importance to develop accurate methods for grasping global trends for the phylogenetic signals that mutually link the various genomes. We therefore derive here the methodological concept of genome trees based on protein conservation profiles in multiple species. The basic idea in this derivation is that the multi-component "presence-absence" protein conservation profiles permit tracking of common evolutionary histories of genes across multiple genomes. We show that a significant reduction in informational redundancy is achieved by considering only the subset of distinct conservation profiles. Beyond these basic ideas, we point out various pitfalls and limitations associated with the data handling, paving the way for further improvements. As an illustration for the methods, we analyze a genome tree based on the above principles, along with a series of other trees derived from the same data and based on pair-wise comparisons (ancestral duplication-conservation and shared orthologs. In all trees we observe a sharp discrimination between the three primary domains of life: Bacteria, Archaea, and Eukarya. The new genome tree, based on conservation profiles, displays a significant correspondence with classically recognized taxonomical groupings, along with a series of departures from such conventional clusterings.

  4. Genome engineering in Vibrio cholerae

    DEFF Research Database (Denmark)

    Val, Marie-Eve; Skovgaard, Ole; Ducos-Galand, Magaly

    2012-01-01

    Although bacteria with multipartite genomes are prevalent, our knowledge of the mechanisms maintaining their genome is very limited, and much remains to be learned about the structural and functional interrelationships of multiple chromosomes. Owing to its bi-chromosomal genome architecture and its....... This difficulty was surmounted using a unique and powerful strategy based on massive rearrangement of prokaryotic genomes. We developed a site-specific recombination-based engineering tool, which allows targeted, oriented, and reciprocal DNA exchanges. Using this genetic tool, we obtained a panel of V. cholerae...

  5. A REVIEW ON GENOME EDITING

    OpenAIRE

    Akshay Patil, Latesh Patil, H. P. Suryawanshi, S. P. Pawar

    2017-01-01

    The Present Review report contains the information about Genome Editing. In this report genome editing is illustrated at the basic level for better understanding. It contains History of Genome Editing from 1800 to Current day i.e. from concept of DNA till current time. Genome editing is an technique to make every human smarter not our choice, by customizing next generation the way we want it to be like to be look and also the intellectual capacity. In this Concept, the viral Immunity is used ...

  6. Genome Writing: Current Progress and Related Applications

    Directory of Open Access Journals (Sweden)

    Yueqiang Wang

    2018-02-01

    Full Text Available The ultimate goal of synthetic biology is to build customized cells or organisms to meet specific industrial or medical needs. The most important part of the customized cell is a synthetic genome. Advanced genomic writing technologies are required to build such an artificial genome. Recently, the partially-completed synthetic yeast genome project represents a milestone in this field. In this mini review, we briefly introduce the techniques for de novo genome synthesis and genome editing. Furthermore, we summarize recent research progresses and highlight several applications in the synthetic genome field. Finally, we discuss current challenges and future prospects. Keywords: Synthetic biology, Genome writing, Genome editing, Bioethics, Biosafety

  7. Comparative genomics of Lactobacillus and other LAB

    DEFF Research Database (Denmark)

    Wassenaar, Trudy M.; Lukjancenko, Oksana

    2014-01-01

    The genomes of 66 LABs, belonging to five different genera, were compared for genome size and gene content. The analyzed genomes included 37 Lactobacillus genomes of 17 species, six Lactococcus lactis genomes, four Leuconostoc genomes of three species, six Streptococcus genomes of two species...... that of the others, with the two Streptococcus species having the shortest genomes. The widest distribution in genome content was observed for Lactobacillus. The number of tRNA and rRNA gene copies varied considerably, with exceptional high numbers observed for Lb. delbrueckii, while these numbers were relatively...

  8. Mesoscale, Radiometrically Referenced, Multi-Temporal Hyperspectral Data for Co2 Leak Detection by Locating Spatial Variation of Biophysically Relevant Parameters

    Science.gov (United States)

    McCann, Cooper Patrick

    Low-cost flight-based hyperspectral imaging systems have the potential to provide valuable information for ecosystem and environmental studies as well as aide in land management and land health monitoring. This thesis describes (1) a bootstrap method of producing mesoscale, radiometrically-referenced hyperspectral data using the Landsat surface reflectance (LaSRC) data product as a reference target, (2) biophysically relevant basis functions to model the reflectance spectra, (3) an unsupervised classification technique based on natural histogram splitting of these biophysically relevant parameters, and (4) local and multi-temporal anomaly detection. The bootstrap method extends standard processing techniques to remove uneven illumination conditions between flight passes, allowing the creation of radiometrically self-consistent data. Through selective spectral and spatial resampling, LaSRC data is used as a radiometric reference target. Advantages of the bootstrap method include the need for minimal site access, no ancillary instrumentation, and automated data processing. Data from a flight on 06/02/2016 is compared with concurrently collected ground based reflectance spectra as a means of validation achieving an average error of 2.74%. Fitting reflectance spectra using basis functions, based on biophysically relevant spectral features, allows both noise and data reductions while shifting information from spectral bands to biophysical features. Histogram splitting is used to determine a clustering based on natural splittings of these fit parameters. The Indian Pines reference data enabled comparisons of the efficacy of this technique to established techniques. The splitting technique is shown to be an improvement over the ISODATA clustering technique with an overall accuracy of 34.3/19.0% before merging and 40.9/39.2% after merging. This improvement is also seen as an improvement of kappa before/after merging of 24.8/30.5 for the histogram splitting technique

  9. Whole genome analysis of a Vietnamese trio

    Indian Academy of Sciences (India)

    2015-02-04

    Feb 4, 2015 ... 2008), Korean genome (Ahn et al. 2009), Japanese genome. (Fujimoto et al. 2010), Pakistani genome (Azim et al. 2013),. Turkish genome (Dogan et al. 2014) and Russian genome. (Skryabin et al. 2009). Being the 14th largest country by population in the world,. Vietnam has about 90 million people of 54 ...

  10. Genome Update: alignment of bacterial chromosomes

    DEFF Research Database (Denmark)

    Ussery, David; Jensen, Mette; Poulsen, Tine Rugh

    2004-01-01

    There are four new microbial genomes listed in this month's Genome Update, three belonging to Gram-positive bacteria and one belonging to an archaeon that lives at pH 0; all of these genomes are listed in Table 1⇓. The method of genome comparison this month is that of genome alignment and, as an ...

  11. Development of bioinformatics resources for display and analysis of copy number and other structural variants in the human genome.

    Science.gov (United States)

    Zhang, J; Feuk, L; Duggan, G E; Khaja, R; Scherer, S W

    2006-01-01

    The discovery of an abundance of copy number variants (CNVs; gains and losses of DNA sequences >1 kb) and other structural variants in the human genome is influencing the way research and diagnostic analyses are being designed and interpreted. As such, comprehensive databases with the most relevant information will be critical to fully understand the results and have impact in a diverse range of disciplines ranging from molecular biology to clinical genetics. Here, we describe the development of bioinformatics resources to facilitate these studies. The Database of Genomic Variants (http://projects.tcag.ca/variation/) is a comprehensive catalogue of structural variation in the human genome. The database currently contains 1,267 regions reported to contain copy number variation or inversions in apparently healthy human cases. We describe the current contents of the database and how it can serve as a resource for interpretation of array comparative genomic hybridization (array CGH) and other DNA copy imbalance data. We also present the structure of the database, which was built using a new data modeling methodology termed Cross-Referenced Tables (XRT). This is a generic and easy-to-use platform, which is strong in handling textual data and complex relationships. Web-based presentation tools have been built allowing publication of XRT data to the web immediately along with rapid sharing of files with other databases and genome browsers. We also describe a novel tool named eFISH (electronic fluorescence in situ hybridization) (http://projects.tcag.ca/efish/), a BLAST-based program that was developed to facilitate the choice of appropriate clones for FISH and CGH experiments, as well as interpretation of results in which genomic DNA probes are used in hybridization-based experiments. Copyright (c) 2006 S. Karger AG, Basel.

  12. Genomics and cardiovascular disease.

    Science.gov (United States)

    Frazier, Lorraine; Johnson, Rolanda L; Sparks, Elizabeth

    2005-01-01

    To describe genetic knowledge and discovery in the area of cardiovascular disease (CVD) and to discuss how these new advances will influence the clinical care of affected people. A selective review of the literature is presented on the disease mechanism of both the Mendelian and multifactorial genetic cardiovascular conditions. A case study approach is used to illustrate how the genetic paradigm affects the healthcare experience of a family affected with familial hypertrophic cardiomyopathy. The current state of CVD treatment remains complex. An understanding of genomic concepts and a genome-based approach is necessary to determine: (a) the risk of CVD susceptibility beyond traditional risk factors; (b) early detection of illness; (c) response to treatment; and (d) molecular taxonomy of the disease. The results of genetic research, education, and teaching will lead to a new understanding of genes and pathways, resulting in powerful new therapeutic approaches to CVD. The challenge is to translate genetic discoveries into clinical practice that ultimately leads to preventing CVD and reducing mortality.

  13. ENCODE whole-genome data in the UCSC Genome Browser

    Science.gov (United States)

    Rosenbloom, Kate R.; Dreszer, Timothy R.; Pheasant, Michael; Barber, Galt P.; Meyer, Laurence R.; Pohl, Andy; Raney, Brian J.; Wang, Ting; Hinrichs, Angie S.; Zweig, Ann S.; Fujita, Pauline A.; Learned, Katrina; Rhead, Brooke; Smith, Kayla E.; Kuhn, Robert M.; Karolchik, Donna; Haussler, David; Kent, W. James

    2010-01-01

    The Encyclopedia of DNA Elements (ENCODE) project is an international consortium of investigators funded to analyze the human genome with the goal of producing a comprehensive catalog of functional elements. The ENCODE Data Coordination Center at The University of California, Santa Cruz (UCSC) is the primary repository for experimental results generated by ENCODE investigators. These results are captured in the UCSC Genome Bioinformatics database and download server for visualization and data mining via the UCSC Genome Browser and companion tools (Rhead et al. The UCSC Genome Browser Database: update 2010, in this issue). The ENCODE web portal at UCSC (http://encodeproject.org or http://genome.ucsc.edu/ENCODE) provides information about the ENCODE data and convenient links for access. PMID:19920125

  14. A Taste of Algal Genomes from the Joint Genome Institute

    Energy Technology Data Exchange (ETDEWEB)

    Kuo, Alan; Grigoriev, Igor

    2012-06-17

    Algae play profound roles in aquatic food chains and the carbon cycle, can impose health and economic costs through toxic blooms, provide models for the study of symbiosis, photosynthesis, and eukaryotic evolution, and are candidate sources for bio-fuels; all of these research areas are part of the mission of DOE's Joint Genome Institute (JGI). To date JGI has sequenced, assembled, annotated, and released to the public the genomes of 18 species and strains of algae, sampling almost all of the major clades of photosynthetic eukaryotes. With more algal genomes currently undergoing analysis, JGI continues its commitment to driving forward basic and applied algal science. Among these ongoing projects are the pan-genome of the dominant coccolithophore Emiliania huxleyi, the interrelationships between the 4 genomes in the nucleomorph-containing Bigelowiella natans and Guillardia theta, and the search for symbiosis genes of lichens.

  15. Genomic selection: genome-wide prediction in plant improvement.

    Science.gov (United States)

    Desta, Zeratsion Abera; Ortiz, Rodomiro

    2014-09-01

    Association analysis is used to measure relations between markers and quantitative trait loci (QTL). Their estimation ignores genes with small effects that trigger underpinning quantitative traits. By contrast, genome-wide selection estimates marker effects across the whole genome on the target population based on a prediction model developed in the training population (TP). Whole-genome prediction models estimate all marker effects in all loci and capture small QTL effects. Here, we review several genomic selection (GS) models with respect to both the prediction accuracy and genetic gain from selection. Phenotypic selection or marker-assisted breeding protocols can be replaced by selection, based on whole-genome predictions in which phenotyping updates the model to build up the prediction accuracy. Copyright © 2014 Elsevier Ltd. All rights reserved.

  16. Parasite Genome Projects and the Trypanosoma cruzi Genome Initiative

    Directory of Open Access Journals (Sweden)

    Wim Degrave

    1997-11-01

    Full Text Available Since the start of the human genome project, a great number of genome projects on other "model" organism have been initiated, some of them already completed. Several initiatives have also been started on parasite genomes, mainly through support from WHO/TDR, involving North-South and South-South collaborations, and great hopes are vested in that these initiatives will lead to new tools for disease control and prevention, as well as to the establishment of genomic research technology in developing countries. The Trypanosoma cruzi genome project, using the clone CL-Brener as starting point, has made considerable progress through the concerted action of more than 20 laboratories, most of them in the South. A brief overview of the current state of the project is given

  17. Genome update: the 1000th genome - a cautionary tale

    DEFF Research Database (Denmark)

    Lagesen, Karin; Ussery, David; Wassenaar, Gertrude Maria

    2010-01-01

    There are now more than 1000 sequenced prokaryotic genomes deposited in public databases and available for analysis. Currently, although the sequence databases GenBank, DNA Database of Japan and EMBL are synchronized continually, there are slight differences in content at the genomes level...... for a variety of logistical reasons, including differences in format and loading errors, such as those caused by file transfer protocol interruptions. This means that the 1000th genome will be different in the various databases. Some of the data on the highly accessed web pages are inaccurate, leading to false......, of the 1000 genomes available, not a single protein is conserved across all genomes. Excluding the members of the Archaea, only a total of four genes are conserved in all bacteria: two protein genes and two RNA genes....

  18. Genome graphs and the evolution of genome inference

    Science.gov (United States)

    Paten, Benedict; Novak, Adam M.; Eizenga, Jordan M.; Garrison, Erik

    2017-01-01

    The human reference genome is part of the foundation of modern human biology and a monumental scientific achievement. However, because it excludes a great deal of common human variation, it introduces a pervasive reference bias into the field of human genomics. To reduce this bias, it makes sense to draw on representative collections of human genomes, brought together into reference cohorts. There are a number of techniques to represent and organize data gleaned from these cohorts, many using ideas implicitly or explicitly borrowed from graph-based models. Here, we survey various projects underway to build and apply these graph-based structures—which we collectively refer to as genome graphs—and discuss the improvements in read mapping, variant calling, and haplotype determination that genome graphs are expected to produce. PMID:28360232

  19. Theory of microbial genome evolution

    Science.gov (United States)

    Koonin, Eugene

    Bacteria and archaea have small genomes tightly packed with protein-coding genes. This compactness is commonly perceived as evidence of adaptive genome streamlining caused by strong purifying selection in large microbial populations. In such populations, even the small cost incurred by nonfunctional DNA because of extra energy and time expenditure is thought to be sufficient for this extra genetic material to be eliminated by selection. However, contrary to the predictions of this model, there exists a consistent, positive correlation between the strength of selection at the protein sequence level, measured as the ratio of nonsynonymous to synonymous substitution rates, and microbial genome size. By fitting the genome size distributions in multiple groups of prokaryotes to predictions of mathematical models of population evolution, we show that only models in which acquisition of additional genes is, on average, slightly beneficial yield a good fit to genomic data. Thus, the number of genes in prokaryotic genomes seems to reflect the equilibrium between the benefit of additional genes that diminishes as the genome grows and deletion bias. New genes acquired by microbial genomes, on average, appear to be adaptive. Evolution of bacterial and archaeal genomes involves extensive horizontal gene transfer and gene loss. Many microbes have open pangenomes, where each newly sequenced genome contains more than 10% `ORFans', genes without detectable homologues in other species. A simple, steady-state evolutionary model reveals two sharply distinct classes of microbial genes, one of which (ORFans) is characterized by effectively instantaneous gene replacement, whereas the other consists of genes with finite, distributed replacement rates. These findings imply a conservative estimate of at least a billion distinct genes in the prokaryotic genomic universe.

  20. OryzaGenome: Genome Diversity Database of Wild Oryza Species

    KAUST Repository

    Ohyanagi, Hajime

    2015-11-18

    The species in the genus Oryza, encompassing nine genome types and 23 species, are a rich genetic resource and may have applications in deeper genomic analyses aiming to understand the evolution of plant genomes. With the advancement of next-generation sequencing (NGS) technology, a flood of Oryza species reference genomes and genomic variation information has become available in recent years. This genomic information, combined with the comprehensive phenotypic information that we are accumulating in our Oryzabase, can serve as an excellent genotype-phenotype association resource for analyzing rice functional and structural evolution, and the associated diversity of the Oryza genus. Here we integrate our previous and future phenotypic/habitat information and newly determined genotype information into a united repository, named OryzaGenome, providing the variant information with hyperlinks to Oryzabase. The current version of OryzaGenome includes genotype information of 446 O. rufipogon accessions derived by imputation and of 17 accessions derived by imputation-free deep sequencing. Two variant viewers are implemented: SNP Viewer as a conventional genome browser interface and Variant Table as a textbased browser for precise inspection of each variant one by one. Portable VCF (variant call format) file or tabdelimited file download is also available. Following these SNP (single nucleotide polymorphism) data, reference pseudomolecules/ scaffolds/contigs and genome-wide variation information for almost all of the closely and distantly related wild Oryza species from the NIG Wild Rice Collection will be available in future releases. All of the resources can be accessed through http://viewer.shigen.info/oryzagenome/.

  1. Fueling Future with Algal Genomics

    Energy Technology Data Exchange (ETDEWEB)

    Grigoriev, Igor

    2012-07-05

    Algae constitute a major component of fundamental eukaryotic diversity, play profound roles in the carbon cycle, and are prominent candidates for biofuel production. The US Department of Energy Joint Genome Institute (JGI) is leading the world in algal genome sequencing (http://jgi.doe.gov/Algae) and contributes of the algal genome projects worldwide (GOLD database, 2012). The sequenced algal genomes offer catalogs of genes, networks, and pathways. The sequenced first of its kind genomes of a haptophyte E.huxleyii, chlorarachniophyte B.natans, and cryptophyte G.theta fill the gaps in the eukaryotic tree of life and carry unique genes and pathways as well as molecular fossils of secondary endosymbiosis. Natural adaptation to conditions critical for industrial production is encoded in algal genomes, for example, growth of A.anophagefferens at very high cell densities during the harmful algae blooms or a global distribution across diverse environments of E.huxleyii, able to live on sparse nutrients due to its expanded pan-genome. Communications and signaling pathways can be derived from simple symbiotic systems like lichens or complex marine algae metagenomes. Collectively these datasets derived from algal genomics contribute to building a comprehensive parts list essential for algal biofuel development.

  2. Comparative genomic hybridization: practical guidelines.

    NARCIS (Netherlands)

    Jeuken, J.W.M.; Sprenger, S.H.; Wesseling, P.

    2002-01-01

    Comparative genomic hybridization (CGH) is a technique used to identify copy number changes throughout a genome. Until now, hundreds of CGH studies have been published reporting chromosomal imbalances in a large variety of human neoplasms. Additionally, technical improvements of specific steps in a

  3. Cocoa/Cotton Comparative Genomics

    Science.gov (United States)

    With genome sequence from two members of the Malvaceae family recently made available, we are exploring syntenic relationships, gene content, and evolutionary trajectories between the cacao and cotton genomes. An assembly of cacao (Theobroma cacao) using Illumina and 454 sequence technology yielded ...

  4. Future Health Applications of Genomics

    Science.gov (United States)

    McBride, Colleen M.; Bowen, Deborah; Brody, Lawrence C.; Condit, Celeste M.; Croyle, Robert T.; Gwinn, Marta; Khoury, Muin J.; Koehly, Laura M.; Korf, Bruce R.; Marteau, Theresa M.; McLeroy, Kenneth; Patrick, Kevin; Valente, Thomas W.

    2014-01-01

    Despite the quickening momentum of genomic discovery, the communication, behavioral, and social sciences research needed for translating this discovery into public health applications has lagged behind. The National Human Genome Research Institute held a 2-day workshop in October 2008 convening an interdisciplinary group of scientists to recommend forward-looking priorities for translational research. This research agenda would be designed to redress the top three risk factors (tobacco use, poor diet, and physical inactivity) that contribute to the four major chronic diseases (heart disease, type 2 diabetes, lung disease, and many cancers) and account for half of all deaths worldwide. Three priority research areas were identified: (1) improving the public’s genetic literacy in order to enhance consumer skills; (2) gauging whether genomic information improves risk communication and adoption of healthier behaviors more than current approaches; and (3) exploring whether genomic discovery in concert with emerging technologies can elucidate new behavioral intervention targets. Important crosscutting themes also were identified, including the need to: (1) anticipate directions of genomic discovery; (2) take an agnostic scientific perspective in framing research questions asking whether genomic discovery adds value to other health promotion efforts; and (3) consider multiple levels of influence and systems that contribute to important public health problems. The priorities and themes offer a framework for a variety of stakeholders, including those who develop priorities for research funding, interdisciplinary teams engaged in genomics research, and policymakers grappling with how to use the products born of genomics research to address public health challenges. PMID:20409503

  5. Genome editing in cardiovascular diseases.

    Science.gov (United States)

    Strong, Alanna; Musunuru, Kiran

    2017-01-01

    Genome-editing tools, which include zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated 9 (Cas9) systems, have emerged as an invaluable technology to achieve somatic and germline genomic manipulation in cells and model organisms for multiple applications, including the creation of knockout alleles, introducing desired mutations into genomic DNA, and inserting novel transgenes. Genome editing is being rapidly adopted into all fields of biomedical research, including the cardiovascular field, where it has facilitated a greater understanding of lipid metabolism, electrophysiology, cardiomyopathies, and other cardiovascular disorders, has helped to create a wider variety of cellular and animal models, and has opened the door to a new class of therapies. In this Review, we discuss the applications of genome-editing technology throughout cardiovascular disease research and the prospect of in vivo genome-editing therapies in the future. We also describe some of the existing limitations of genome-editing tools that will need to be addressed if cardiovascular genome editing is to achieve its full scientific and therapeutic potential.

  6. The promise of insect genomics

    DEFF Research Database (Denmark)

    Grimmelikhuijzen, Cornelis J P; Cazzamali, Giuseppe; Williamson, Michael

    2007-01-01

    Insects are the largest animal group in the world and are ecologically and economically extremely important. This importance of insects is reflected by the existence of currently 24 insect genome projects. Our perspective discusses the state-of-the-art of these genome projects and the impacts...

  7. Comparative Genomics of the Cucurbitaceae

    Science.gov (United States)

    The genome size for watermelon, melon, cucumber, and pumpkin is 425, 454, 367, and 502 Mbp, respectively, and considered medium size as compared with most other crops. Whole-genome duplication is common in angiosperm plants. Research has revealed a paleohexaploidy (') event in the common ancestor of...

  8. Bioinformatics of genomic association mapping

    NARCIS (Netherlands)

    Vaez Barzani, Ahmad

    2015-01-01

    In this thesis we present an overview of bioinformatics-based approaches for genomic association mapping, with emphasis on human quantitative traits and their contribution to complex diseases. We aim to provide a comprehensive walk-through of the classic steps of genomic association mapping

  9. International genomic evaluation methods for dairy cattle

    Science.gov (United States)

    Background Genomic evaluations are rapidly replacing traditional evaluation systems used for dairy cattle selection. Economies of scale in genomics promote cooperation across country borders. Genomic information can be transferred across countries using simple conversion equations, by modifying mult...

  10. Open chromatin in plant genomes.

    Science.gov (United States)

    Zhang, Wenli; Zhang, Tao; Wu, Yufeng; Jiang, Jiming

    2014-01-01

    Sensitivity to DNase I digestion is an indicator of the accessibility and configuration of chromatin in eukaryotic genomes. Open chromatin exhibits high sensitivity to DNase I cleavage. DNase I hypersensitive sites (DHSs) in eukaryotic genomes can be identified through DNase I treatment followed by sequencing (DNase-seq). DHSs are most frequently associated with various cis-regulatory DNA elements, including promoters, enhancers, and silencers in both animal and plant genomes. Genome-wide identification of DHSs provides an efficient method to interpret previously un-annotated regulatory DNA sequences. In this review, we provide an overview of the historical perspective of DHS research in eukaryotes. We summarize the main achievements of DHS research in model animal species and review the recent progress of DHS research in plants. We finally discuss possible future directions of using DHS as a tool in plant genomics research. © 2014 S. Karger AG, Basel.

  11. [Trends of angiosperm genome evolution].

    Science.gov (United States)

    Sheremet'ev, S N; Gamaleĭ, Iu V; Slemnev, N N

    2011-01-01

    Direction of evolutionary variability of parameters of genome size and structurally functional activity of plants on life forms groups and angiosperms taxa are analyzed. It is shown that, in the Cretaceous-Cenozoic, their nuclear genome tended to increase. Functional genome efficiency (intensity of functions per 1 pg of DNA) decreased from as much as possible high at trees and lianas of rain and monsoonal forests of the Paleogene to minimum at shrubs, perennial and annual grasses of meadow-steppe vegetation which had appeared in the neogene. Important for the vegetation environmental changes in temperature, humidity and CO2 concentration in an adverse direction are discussed as the cause of evolutionary genome size growth and decrease in its functional efficiency. Price for phylogenetic adaptogenesis of angiosperms to the step Cenozoic climate cooling was 4-fold and more genome growth.

  12. Allele coding in genomic evaluation

    DEFF Research Database (Denmark)

    Standen, Ismo; Christensen, Ole Fredslund

    2011-01-01

    Genomic data are used in animal breeding to assist genetic evaluation. Several models to estimate genomic breeding values have been studied. In general, two approaches have been used. One approach estimates the marker effects first and then, genomic breeding values are obtained by summing marker...... effects. In the second approach, genomic breeding values are estimated directly using an equivalent model with a genomic relationship matrix. Allele coding is the method chosen to assign values to the regression coefficients in the statistical model. A common allele coding is zero for the homozygous...... this centered allele coding. This study considered effects of different allele coding methods on inference. Both marker-based and equivalent models were considered, and restricted maximum likelihood and Bayesian methods were used in inference. \\paragraph*{Results:} Theoretical derivations showed that parameter...

  13. Pathophysiology of MDS: genomic aberrations.

    Science.gov (United States)

    Ichikawa, Motoshi

    2016-01-01

    Myelodysplastic syndromes (MDS) are characterized by clonal proliferation of hematopoietic stem/progenitor cells and their apoptosis, and show a propensity to progress to acute myelogenous leukemia (AML). Although MDS are recognized as neoplastic diseases caused by genomic aberrations of hematopoietic cells, the details of the genetic abnormalities underlying disease development have not as yet been fully elucidated due to difficulties in analyzing chromosomal abnormalities. Recent advances in comprehensive analyses of disease genomes including whole-genome sequencing technologies have revealed the genomic abnormalities in MDS. Surprisingly, gene mutations were found in approximately 80-90% of cases with MDS, and the novel mutations discovered with these technologies included previously unknown, MDS-specific, mutations such as those of the genes in the RNA-splicing machinery. It is anticipated that these recent studies will shed new light on the pathophysiology of MDS due to genomic aberrations.

  14. Genomic methods take the plunge

    DEFF Research Database (Denmark)

    Cammen, Kristina M.; Andrews, Kimberly R.; Carroll, Emma L.

    2016-01-01

    The dramatic increase in the application of genomic techniques to non-model organisms (NMOs) over the past decade has yielded numerous valuable contributions to evolutionary biology and ecology, many of which would not have been possible with traditional genetic markers. We review this recent...... progression with a particular focus on genomic studies of marine mammals, a group of taxa that represent key macroevolutionary transitions from terrestrial to marine environments and for which available genomic resources have recently undergone notable rapid growth. Genomic studies of NMOs utilize...... an expanding range of approaches, including whole genome sequencing, restriction site-associated DNA sequencing, array-based sequencing of single nucleotide polymorphisms and target sequence probes (e.g., exomes), and transcriptome sequencing. These approaches generate different types and quantities of data...

  15. [Preface for genome editing special issue].

    Science.gov (United States)

    Gu, Feng; Gao, Caixia

    2017-10-25

    Genome editing technology, as an innovative biotechnology, has been widely used for editing the genome from model organisms, animals, plants and microbes. CRISPR/Cas9-based genome editing technology shows its great value and potential in the dissection of functional genomics, improved breeding and genetic disease treatment. In the present special issue, the principle and application of genome editing techniques has been summarized. The advantages and disadvantages of the current genome editing technology and future prospects would also be highlighted.

  16. Privacy in the Genomic Era

    Science.gov (United States)

    NAVEED, MUHAMMAD; AYDAY, ERMAN; CLAYTON, ELLEN W.; FELLAY, JACQUES; GUNTER, CARL A.; HUBAUX, JEAN-PIERRE; MALIN, BRADLEY A.; WANG, XIAOFENG

    2015-01-01

    Genome sequencing technology has advanced at a rapid pace and it is now possible to generate highly-detailed genotypes inexpensively. The collection and analysis of such data has the potential to support various applications, including personalized medical services. While the benefits of the genomics revolution are trumpeted by the biomedical community, the increased availability of such data has major implications for personal privacy; notably because the genome has certain essential features, which include (but are not limited to) (i) an association with traits and certain diseases, (ii) identification capability (e.g., forensics), and (iii) revelation of family relationships. Moreover, direct-to-consumer DNA testing increases the likelihood that genome data will be made available in less regulated environments, such as the Internet and for-profit companies. The problem of genome data privacy thus resides at the crossroads of computer science, medicine, and public policy. While the computer scientists have addressed data privacy for various data types, there has been less attention dedicated to genomic data. Thus, the goal of this paper is to provide a systematization of knowledge for the computer science community. In doing so, we address some of the (sometimes erroneous) beliefs of this field and we report on a survey we conducted about genome data privacy with biomedical specialists. Then, after characterizing the genome privacy problem, we review the state-of-the-art regarding privacy attacks on genomic data and strategies for mitigating such attacks, as well as contextualizing these attacks from the perspective of medicine and public policy. This paper concludes with an enumeration of the challenges for genome data privacy and presents a framework to systematize the analysis of threats and the design of countermeasures as the field moves forward. PMID:26640318

  17. Privacy in the Genomic Era.

    Science.gov (United States)

    Naveed, Muhammad; Ayday, Erman; Clayton, Ellen W; Fellay, Jacques; Gunter, Carl A; Hubaux, Jean-Pierre; Malin, Bradley A; Wang, Xiaofeng

    2015-09-01

    Genome sequencing technology has advanced at a rapid pace and it is now possible to generate highly-detailed genotypes inexpensively. The collection and analysis of such data has the potential to support various applications, including personalized medical services. While the benefits of the genomics revolution are trumpeted by the biomedical community, the increased availability of such data has major implications for personal privacy; notably because the genome has certain essential features, which include (but are not limited to) (i) an association with traits and certain diseases, (ii) identification capability (e.g., forensics), and (iii) revelation of family relationships. Moreover, direct-to-consumer DNA testing increases the likelihood that genome data will be made available in less regulated environments, such as the Internet and for-profit companies. The problem of genome data privacy thus resides at the crossroads of computer science, medicine, and public policy. While the computer scientists have addressed data privacy for various data types, there has been less attention dedicated to genomic data. Thus, the goal of this paper is to provide a systematization of knowledge for the computer science community. In doing so, we address some of the (sometimes erroneous) beliefs of this field and we report on a survey we conducted about genome data privacy with biomedical specialists. Then, after characterizing the genome privacy problem, we review the state-of-the-art regarding privacy attacks on genomic data and strategies for mitigating such attacks, as well as contextualizing these attacks from the perspective of medicine and public policy. This paper concludes with an enumeration of the challenges for genome data privacy and presents a framework to systematize the analysis of threats and the design of countermeasures as the field moves forward.

  18. The South Asian genome.

    Directory of Open Access Journals (Sweden)

    John C Chambers

    Full Text Available The genetic sequence variation of people from the Indian subcontinent who comprise one-quarter of the world's population, is not well described. We carried out whole genome sequencing of 168 South Asians, along with whole-exome sequencing of 147 South Asians to provide deeper characterisation of coding regions. We identify 12,962,155 autosomal sequence variants, including 2,946,861 new SNPs and 312,738 novel indels. This catalogue of SNPs and indels amongst South Asians provides the first comprehensive map of genetic variation in this major human population, and reveals evidence for selective pressures on genes involved in skin biology, metabolism, infection and immunity. Our results will accelerate the search for the genetic variants underlying susceptibility to disorders such as type-2 diabetes and cardiovascular disease which are highly prevalent amongst South Asians.

  19. Inheritance of the yeast mitochondrial genome

    DEFF Research Database (Denmark)

    Piskur, Jure

    1994-01-01

    Mitochondrion, extrachromosomal genetics, intergenic sequences, genome size, mitochondrial DNA, petite mutation, yeast......Mitochondrion, extrachromosomal genetics, intergenic sequences, genome size, mitochondrial DNA, petite mutation, yeast...

  20. Plantagora: modeling whole genome sequencing and assembly of plant genomes.

    Directory of Open Access Journals (Sweden)

    Roger Barthelson

    Full Text Available BACKGROUND: Genomics studies are being revolutionized by the next generation sequencing technologies, which have made whole genome sequencing much more accessible to the average researcher. Whole genome sequencing with the new technologies is a developing art that, despite the large volumes of data that can be produced, may still fail to provide a clear and thorough map of a genome. The Plantagora project was conceived to address specifically the gap between having the technical tools for genome sequencing and knowing precisely the best way to use them. METHODOLOGY/PRINCIPAL FINDINGS: For Plantagora, a platform was created for generating simulated reads from several different plant genomes of different sizes. The resulting read files mimicked either 454 or Illumina reads, with varying paired end spacing. Thousands of datasets of reads were created, most derived from our primary model genome, rice chromosome one. All reads were assembled with different software assemblers, including Newbler, Abyss, and SOAPdenovo, and the resulting assemblies were evaluated by an extensive battery of metrics chosen for these studies. The metrics included both statistics of the assembly sequences and fidelity-related measures derived by alignment of the assemblies to the original genome source for the reads. The results were presented in a website, which includes a data graphing tool, all created to help the user compare rapidly the feasibility and effectiveness of different sequencing and assembly strategies prior to testing an approach in the lab. Some of our own conclusions regarding the different strategies were also recorded on the website. CONCLUSIONS/SIGNIFICANCE: Plantagora provides a substantial body of information for comparing different approaches to sequencing a plant genome, and some conclusions regarding some of the specific approaches. Plantagora also provides a platform of metrics and tools for studying the process of sequencing and assembly

  1. The Perennial Ryegrass GenomeZipper – Targeted Use of Genome Resources for Comparative Grass Genomics

    DEFF Research Database (Denmark)

    Pfeiffer, Matthias; Martis, Mihaela; Asp, Torben

    2013-01-01

    Whole-genome sequences established for model and major crop species constitute a key resource for advanced genomic research. For outbreeding forage and turf grass species like ryegrasses (Lolium spp.), such resources have yet to be developed. Here, we present a model of the perennial ryegrass (Lo...

  2. Comparative Genomics Reveals High Genomic Diversity in the Genus Photobacterium

    DEFF Research Database (Denmark)

    Machado, Henrique; Gram, Lone

    2017-01-01

    Vibrionaceae is a large marine bacterial family, which can constitute up to 50% of the prokaryotic population in marine waters. Photobacterium is the second largest genus in the family and we used comparative genomics on 35 strains representing 16 of the 28 species described so far, to understand...... the genomic diversity present in the Photobacterium genus. Such understanding is important for ecophysiology studies of the genus. We used whole genome sequences to evaluate phylogenetic relationships using several analyses (16S rRNA, MLSA, fur, amino-acid usage, ANI), which allowed us to identify two...

  3. Comparative genomics reveals insights into avian genome evolution and adaptation

    DEFF Research Database (Denmark)

    Zhang, Guojie; Li, Cai; Li, Qiye

    2014-01-01

    Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size...... this pattern of conservation, we detected many non-neutral evolutionary changes in protein-coding genes and noncoding regions. These analyses reveal that pan-avian genomic diversity covaries with adaptations to different lifestyles and convergent evolution of traits....

  4. Dual-lifetime referencing (DLR: a powerful method for on-line measurement of internal pH in carrier-bound immobilized biocatalysts

    Directory of Open Access Journals (Sweden)

    Boniello Caterina

    2012-03-01

    Full Text Available Abstract Background Industrial-scale biocatalytic synthesis of fine chemicals occurs preferentially as continuous processes employing immobilized enzymes on insoluble porous carriers. Diffusional effects in these systems often create substrate and product concentration gradients between bulk liquid and the carrier. Moreover, some widely-used biotransformation processes induce changes in proton concentration. Unlike the bulk pH, which is usually controlled at a suitable value, the intraparticle pH of immobilized enzymes may deviate significantly from its activity and stability optima. The magnitude of the resulting pH gradient depends on the ratio of characteristic times for enzymatic reaction and on mass transfer (the latter is strongly influenced by geometrical features of the porous carrier. Design and selection of optimally performing enzyme immobilizates would therefore benefit largely from experimental studies of the intraparticle pH environment. Here, a simple and non-invasive method based on dual-lifetime referencing (DLR for pH determination in immobilized enzymes is introduced. The technique is applicable to other systems in which particles are kept in suspension by agitation. Results The DLR method employs fluorescein as pH-sensitive luminophore and Ru(II tris(4,7-diphenyl-1,10-phenantroline, abbreviated Ru(dpp, as the reference luminophore. Luminescence intensities of the two luminophores are converted into an overall phase shift suitable for pH determination in the range 5.0-8.0. Sepabeads EC-EP were labeled by physically incorporating lipophilic variants of the two luminophores into their polymeric matrix. These beads were employed as carriers for immobilization of cephalosporin C amidase (a model enzyme of industrial relevance. The luminophores did not interfere with the enzyme immobilization characteristics. Analytical intraparticle pH determination was optimized for sensitivity, reproducibility and signal stability under

  5. Individual genetic and genomic research results and the tradition of informed consent: exploring US review board guidance.

    Science.gov (United States)

    Simon, Christian; Shinkunas, Laura A; Brandt, Debra; Williams, Janet K

    2012-07-01

    Genomic research is challenging the tradition of informed consent. Genomic researchers in the USA, Canada and parts of Europe are encouraged to use informed consent to address the prospect of disclosing individual research results (IRRs) to study participants. In the USA, no national policy exists to direct this use of informed consent, and it is unclear how local institutional review boards (IRBs) may want researchers to respond. To explore publicly accessible IRB websites for guidance in this area, using summative content analysis. Three types of research results were addressed in 45 informed consent templates and instructions from 20 IRBs based at centres conducting genomic research: (1) IRRs in general, (2) incidental findings (IFs) and (3) a broad and unspecified category of 'significant new findings' (SNFs). IRRs were more frequently referenced than IFs or SNFs. Most documents stated that access to IRRs would not be an option for research participants. These non-disclosure statements were found to coexist in some documents with statements that SNFs would be disclosed to participants if related to their willingness to participate in research. The median readability of template language on IRRs, IFs and SNFs exceeded a ninth-grade level. IRB guidance may downplay the possibility of IFs and contain conflicting messages on IRR non-disclosure and SNF disclosure. IRBs may need to clarify why separate IRR and SNF language should appear in the same consent document. The extent of these issues, nationally and internationally, needs to be determined.

  6. Components of Adenovirus Genome Packaging

    Science.gov (United States)

    Ahi, Yadvinder S.; Mittal, Suresh K.

    2016-01-01

    Adenoviruses (AdVs) are icosahedral viruses with double-stranded DNA (dsDNA) genomes. Genome packaging in AdV is thought to be similar to that seen in dsDNA containing icosahedral bacteriophages and herpesviruses. Specific recognition of the AdV genome is mediated by a packaging domain located close to the left end of the viral genome and is mediated by the viral packaging machinery. Our understanding of the role of various components of the viral packaging machinery in AdV genome packaging has greatly advanced in recent years. Characterization of empty capsids assembled in the absence of one or more components involved in packaging, identification of the unique vertex, and demonstration of the role of IVa2, the putative packaging ATPase, in genome packaging have provided compelling evidence that AdVs follow a sequential assembly pathway. This review provides a detailed discussion on the functions of the various viral and cellular factors involved in AdV genome packaging. We conclude by briefly discussing the roles of the empty capsids, assembly intermediates, scaffolding proteins, portal vertex and DNA encapsidating enzymes in AdV assembly and packaging. PMID:27721809

  7. The genome of Eucalyptus grandis

    Energy Technology Data Exchange (ETDEWEB)

    Myburg, Alexander A.; Grattapaglia, Dario; Tuskan, Gerald A.; Hellsten, Uffe; Hayes, Richard D.; Grimwood, Jane; Jenkins, Jerry; Lindquist, Erika; Tice, Hope; Bauer, Diane; Goodstein, David M.; Dubchak, Inna; Poliakov, Alexandre; Mizrachi, Eshchar; Kullan, Anand R. K.; Hussey, Steven G.; Pinard, Desre; van der Merwe, Karen; Singh, Pooja; van Jaarsveld, Ida; Silva-Junior, Orzenil B.; Togawa, Roberto C.; Pappas, Marilia R.; Faria, Danielle A.; Sansaloni, Carolina P.; Petroli, Cesar D.; Yang, Xiaohan; Ranjan, Priya; Tschaplinski, Timothy J.; Ye, Chu-Yu; Li, Ting; Sterck, Lieven; Vanneste, Kevin; Murat, Florent; Soler, Marçal; Clemente, Hélène San; Saidi, Naijib; Cassan-Wang, Hua; Dunand, Christophe; Hefer, Charles A.; Bornberg-Bauer, Erich; Kersting, Anna R.; Vining, Kelly; Amarasinghe, Vindhya; Ranik, Martin; Naithani, Sushma; Elser, Justin; Boyd, Alexander E.; Liston, Aaron; Spatafora, Joseph W.; Dharmwardhana, Palitha; Raja, Rajani; Sullivan, Christopher; Romanel, Elisson; Alves-Ferreira, Marcio; Külheim, Carsten; Foley, William; Carocha, Victor; Paiva, Jorge; Kudrna, David; Brommonschenkel, Sergio H.; Pasquali, Giancarlo; Byrne, Margaret; Rigault, Philippe; Tibbits, Josquin; Spokevicius, Antanas; Jones, Rebecca C.; Steane, Dorothy A.; Vaillancourt, René E.; Potts, Brad M.; Joubert, Fourie; Barry, Kerrie; Pappas, Georgios J.; Strauss, Steven H.; Jaiswal, Pankaj; Grima-Pettenati, Jacqueline; Salse, Jérôme; Van de Peer, Yves; Rokhsar, Daniel S.; Schmutz, Jeremy

    2014-06-11

    Eucalypts are the world s most widely planted hardwood trees. Their broad adaptability, rich species diversity, fast growth and superior multipurpose wood, have made them a global renewable resource of fiber and energy that mitigates human pressures on natural forests. We sequenced and assembled >94% of the 640 Mbp genome of Eucalyptus grandis into its 11 chromosomes. A set of 36,376 protein coding genes were predicted revealing that 34% occur in tandem duplications, the largest proportion found thus far in any plant genome. Eucalypts also show the highest diversity of genes for plant specialized metabolism that act as chemical defence against biotic agents and provide unique pharmaceutical oils. Resequencing of a set of inbred tree genomes revealed regions of strongly conserved heterozygosity, likely hotspots of inbreeding depression. The resequenced genome of the sister species E. globulus underscored the high inter-specific genome colinearity despite substantial genome size variation in the genus. The genome of E. grandis is the first reference for the early diverging Rosid order Myrtales and is placed here basal to the Eurosids. This resource expands knowledge on the unique biology of large woody perennials and provides a powerful tool to accelerate comparative biology, breeding and biotechnology.

  8. Functional genomics of intracellular bacteria.

    Science.gov (United States)

    de Barsy, Marie; Greub, Gilbert

    2013-07-01

    During the genomic era, a large amount of whole-genome sequences accumulated, which identified many hypothetical proteins of unknown function. Rapidly, functional genomics, which is the research domain that assign a function to a given gene product, has thus been developed. Functional genomics of intracellular pathogenic bacteria exhibit specific peculiarities due to the fastidious growth of most of these intracellular micro-organisms, due to the close interaction with the host cell, due to the risk of contamination of experiments with host cell proteins and, for some strict intracellular bacteria such as Chlamydia, due to the absence of simple genetic system to manipulate the bacterial genome. To identify virulence factors of intracellular pathogenic bacteria, functional genomics often rely on bioinformatic analyses compared with model organisms such as Escherichia coli and Bacillus subtilis. The use of heterologous expression is another common approach. Given the intracellular lifestyle and the many effectors that are used by the intracellular bacteria to corrupt host cell functions, functional genomics is also often targeting the identification of new effectors such as those of the T4SS of Brucella and Legionella.

  9. [Genome editing of industrial microorganism].

    Science.gov (United States)

    Zhu, Linjiang; Li, Qi

    2015-03-01

    Genome editing is defined as highly-effective and precise modification of cellular genome in a large scale. In recent years, such genome-editing methods have been rapidly developed in the field of industrial strain improvement. The quickly-updating methods thoroughly change the old mode of inefficient genetic modification, which is "one modification, one selection marker, and one target site". Highly-effective modification mode in genome editing have been developed including simultaneous modification of multiplex genes, highly-effective insertion, replacement, and deletion of target genes in the genome scale, cut-paste of a large DNA fragment. These new tools for microbial genome editing will certainly be applied widely, and increase the efficiency of industrial strain improvement, and promote the revolution of traditional fermentation industry and rapid development of novel industrial biotechnology like production of biofuel and biomaterial. The technological principle of these genome-editing methods and their applications were summarized in this review, which can benefit engineering and construction of industrial microorganism.

  10. Recurring genomic breaks in independent lineages support genomic fragility

    Directory of Open Access Journals (Sweden)

    Hannenhalli Sridhar

    2006-11-01

    Full Text Available Abstract Background Recent findings indicate that evolutionary breaks in the genome are not randomly distributed, and that certain regions, so-called fragile regions, are predisposed to breakages. Previous approaches to the study of genomic fragility have examined the distribution of breaks, as well as the coincidence of breaks with segmental duplications and repeats, within a single species. In contrast, we investigate whether this regional fragility is an inherent genomic characteristic and is thus conserved over multiple independent lineages. Results We do this by quantifying the extent to which certain genomic regions are disrupted repeatedly in independent lineages. Our investigation, based on Human, Chimp, Mouse, Rat, Dog and Chicken, suggests that the propensity of a chromosomal region to break is significantly correlated among independent lineages, even when covariates are considered. Furthermore, the fragile regions are enriched for segmental duplications. Conclusion Based on a novel methodology, our work provides additional support for the existence of fragile regions.

  11. Genome Modeling System: A Knowledge Management Platform for Genomics.

    Directory of Open Access Journals (Sweden)

    Malachi Griffith

    2015-07-01

    Full Text Available In this work, we present the Genome Modeling System (GMS, an analysis information management system capable of executing automated genome analysis pipelines at a massive scale. The GMS framework provides detailed tracking of samples and data coupled with reliable and repeatable analysis pipelines. The GMS also serves as a platform for bioinformatics development, allowing a large team to collaborate on data analysis, or an individual researcher to leverage the work of others effectively within its data management system. Rather than separating ad-hoc analysis from rigorous, reproducible pipelines, the GMS promotes systematic integration between the two. As a demonstration of the GMS, we performed an integrated analysis of whole genome, exome and transcriptome sequencing data from a breast cancer cell line (HCC1395 and matched lymphoblastoid line (HCC1395BL. These data are available for users to test the software, complete tutorials and develop novel GMS pipeline configurations. The GMS is available at https://github.com/genome/gms.

  12. The bonobo genome compared with the chimpanzee and human genomes

    Science.gov (United States)

    Prüfer, Kay; Munch, Kasper; Hellmann, Ines; Akagi, Keiko; Miller, Jason R.; Walenz, Brian; Koren, Sergey; Sutton, Granger; Kodira, Chinnappa; Winer, Roger; Knight, James R.; Mullikin, James C.; Meader, Stephen J.; Ponting, Chris P.; Lunter, Gerton; Higashino, Saneyuki; Hobolth, Asger; Dutheil, Julien; Karakoç, Emre; Alkan, Can; Sajjadian, Saba; Catacchio, Claudia Rita; Ventura, Mario; Marques-Bonet, Tomas; Eichler, Evan E.; André, Claudine; Atencia, Rebeca; Mugisha, Lawrence; Junhold, Jörg; Patterson, Nick; Siebauer, Michael; Good, Jeffrey M.; Fischer, Anne; Ptak, Susan E.; Lachmann, Michael; Symer, David E.; Mailund, Thomas; Schierup, Mikkel H.; Andrés, Aida M.; Kelso, Janet; Pääbo, Svante

    2012-01-01

    Two African apes are the closest living relatives of humans: the chimpanzee (Pan troglodytes) and the bonobo (Pan paniscus). Although they are similar in many respects, bonobos and chimpanzees differ strikingly in key social and sexual behaviours1–4, and for some of these traits they show more similarity with humans than with each other. Here we report the sequencing and assembly of the bonobo genome to study its evolutionary relationship with the chimpanzee and human genomes. We find that more than three per cent of the human genome is more closely related to either the bonobo or the chimpanzee genome than these are to each other. These regions allow various aspects of the ancestry of the two ape species to be reconstructed. In addition, many of the regions that overlap genes may eventually help us understand the genetic basis of phenotypes that humans share with one of the two apes to the exclusion of the other. PMID:22722832

  13. Implementing Genome-Driven Oncology

    Science.gov (United States)

    Hyman, David M.; Taylor, Barry S.; Baselga, José

    2017-01-01

    Early successes in identifying and targeting individual oncogenic drivers, together with the increasing feasibility of sequencing tumor genomes, have brought forth the promise of genome-driven oncology care. As we expand the breadth and depth of genomic analyses, the biological and clinical complexity of its implementation will be unparalleled. Challenges include target credentialing and validation, implementing drug combinations, clinical trial designs, targeting tumor heterogeneity, and deploying technologies beyond DNA sequencing, among others. We review how contemporary approaches are tackling these challenges and will ultimately serve as an engine for biological discovery and increase our insight into cancer and its treatment. PMID:28187282

  14. Human genome. 1993 Program report

    Energy Technology Data Exchange (ETDEWEB)

    1994-03-01

    The purpose of this report is to update the Human Genome 1991-92 Program Report and provide new information on the DOE genome program to researchers, program managers, other government agencies, and the interested public. This FY 1993 supplement includes abstracts of 60 new or renewed projects and listings of 112 continuing and 28 completed projects. These two reports, taken together, present the most complete published view of the DOE Human Genome Program through FY 1993. Research is progressing rapidly toward 15-year goals of mapping and sequencing the DNA of each of the 24 different human chromosomes.

  15. Capturing prokaryotic dark matter genomes.

    Science.gov (United States)

    Gasc, Cyrielle; Ribière, Céline; Parisot, Nicolas; Beugnot, Réjane; Defois, Clémence; Petit-Biderre, Corinne; Boucher, Delphine; Peyretaillade, Eric; Peyret, Pierre

    2015-12-01

    Prokaryotes are the most diverse and abundant cellular life forms on Earth. Most of them, identified by indirect molecular approaches, belong to microbial dark matter. The advent of metagenomic and single-cell genomic approaches has highlighted the metabolic capabilities of numerous members of this dark matter through genome reconstruction. Thus, linking functions back to the species has revolutionized our understanding of how ecosystem function is sustained by the microbial world. This review will present discoveries acquired through the illumination of prokaryotic dark matter genomes by these innovative approaches. Copyright © 2015 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

  16. Applied Genomics of Foodborne Pathogens

    DEFF Research Database (Denmark)

    This book provides a timely and thorough snapshot into the emerging and fast evolving area of applied genomics of foodborne pathogens. Driven by the drastic advance of whole genome shot gun sequencing (WGS) technologies, genomics applications are becoming increasingly valuable and even essential...... in studying, surveying and controlling foodborne microbial pathogens. The vast opportunities brought by this trend are often at odds with the lack of bioinformatics know-how among food safety and public health professionals, since such expertise is not part of a typical food microbiology curriculum and skill...

  17. Radiation Induced Genomic Instability

    Energy Technology Data Exchange (ETDEWEB)

    Morgan, William F.

    2011-03-01

    Radiation induced genomic instability can be observed in the progeny of irradiated cells multiple generations after irradiation of parental cells. The phenotype is well established both in vivo (Morgan 2003) and in vitro (Morgan 2003), and may be critical in radiation carcinogenesis (Little 2000, Huang et al. 2003). Instability can be induced by both the deposition of energy in irradiated cells as well as by signals transmitted by irradiated (targeted) cells to non-irradiated (non-targeted) cells (Kadhim et al. 1992, Lorimore et al. 1998). Thus both targeted and non-targeted cells can pass on the legacy of radiation to their progeny. However the radiation induced events and cellular processes that respond to both targeted and non-targeted radiation effects that lead to the unstable phenotype remain elusive. The cell system we have used to study radiation induced genomic instability utilizes human hamster GM10115 cells. These cells have a single copy of human chromosome 4 in a background of hamster chromosomes. Instability is evaluated in the clonal progeny of irradiated cells and a clone is considered unstable if it contains three or more metaphase sub-populations involving unique rearrangements of the human chromosome (Marder and Morgan 1993). Many of these unstable clones have been maintained in culture for many years and have been extensively characterized. As initially described by Clutton et al., (Clutton et al. 1996) many of our unstable clones exhibit persistently elevated levels of reactive oxygen species (Limoli et al. 2003), which appear to be due dysfunctional mitochondria (Kim et al. 2006, Kim et al. 2006). Interestingly, but perhaps not surprisingly, our unstable clones do not demonstrate a “mutator phenotype” (Limoli et al. 1997), but they do continue to rearrange their genomes for many years. The limiting factor with this system is the target – the human chromosome. While some clones demonstrate amplification of this chromosome and thus lend

  18. Identification of genomic sites for CRISPR/Cas9-based genome editing in the Vitis vinifera genome

    Science.gov (United States)

    CRISPR/Cas9 has been recently demonstrated as an effective and popular genome editing tool for modifying genomes of human, animals, microorganisms, and plants. Success of such genome editing is highly dependent on the availability of suitable target sites in the genomes to be edited. Many specific t...

  19. Challenges in Whole-Genome Annotation of Pyrosequenced Eukaryotic Genomes

    Energy Technology Data Exchange (ETDEWEB)

    Kuo, Alan; Grigoriev, Igor

    2009-04-17

    Pyrosequencing technologies such as 454/Roche and Solexa/Illumina vastly lower the cost of nucleotide sequencing compared to the traditional Sanger method, and thus promise to greatly expand the number of sequenced eukaryotic genomes. However, the new technologies also bring new challenges such as shorter reads and new kinds and higher rates of sequencing errors, which complicate genome assembly and gene prediction. At JGI we are deploying 454 technology for the sequencing and assembly of ever-larger eukaryotic genomes. Here we describe our first whole-genome annotation of a purely 454-sequenced fungal genome that is larger than a yeast (>30 Mbp). The pezizomycotine (filamentous ascomycote) Aspergillus carbonarius belongs to the Aspergillus section Nigri species complex, members of which are significant as platforms for bioenergy and bioindustrial technology, as members of soil microbial communities and players in the global carbon cycle, and as agricultural toxigens. Application of a modified version of the standard JGI Annotation Pipeline has so far predicted ~;;10k genes. ~;;12percent of these preliminary annotations suffer a potential frameshift error, which is somewhat higher than the ~;;9percent rate in the Sanger-sequenced and conventionally assembled and annotated genome of fellow Aspergillus section Nigri member A. niger. Also,>90percent of A. niger genes have potential homologs in the A. carbonarius preliminary annotation. Weconclude, and with further annotation and comparative analysis expect to confirm, that 454 sequencing strategies provide a promising substrate for annotation of modestly sized eukaryotic genomes. We will also present results of annotation of a number of other pyrosequenced fungal genomes of bioenergy interest.

  20. The Global Cancer Genomics Consortium: interfacing genomics and cancer medicine.

    Science.gov (United States)

    2012-08-01

    The Global Cancer Genomics Consortium (GCGC) is an international collaborative platform that amalgamates cancer biologists, cutting-edge genomics, and high-throughput expertise with medical oncologists and surgical oncologists; they address the most important translational questions that are central to cancer research and treatment. The annual GCGC symposium was held at the Advanced Centre for Treatment Research and Education in Cancer, Mumbai, India, from November 9 to 11, 2011. The symposium showcased international next-generation sequencing efforts that explore cancer-specific transcriptomic changes, single-nucleotide polymorphism, and copy number variations in various types of cancers, as well as the structural genomics approach to develop new therapeutic targets and chemical probes. From the spectrum of studies presented at the symposium, it is evident that the translation of emerging cancer genomics knowledge into clinical applications can only be achieved through the integration of multidisciplinary expertise. In summary, the GCGC symposium provided practical knowledge on structural and cancer genomics approaches, as well as an exclusive platform for focused cancer genomics endeavors. ©2012 AACR.

  1. Palaeohexaploid ancestry for Caryophyllales inferred from extensive gene-based physical and genetic mapping of the sugar beet genome (Beta vulgaris).

    Science.gov (United States)

    Dohm, Juliane C; Lange, Cornelia; Holtgräwe, Daniela; Sörensen, Thomas Rosleff; Borchardt, Dietrich; Schulz, Britta; Lehrach, Hans; Weisshaar, Bernd; Himmelbauer, Heinz

    2012-05-01

    Sugar beet (Beta vulgaris) is an important crop plant that accounts for 30% of the world's sugar production annually. The genus Beta is a distant relative of currently sequenced taxa within the core eudicotyledons; the genomic characterization of sugar beet is essential to make its genome accessible to molecular dissection. Here, we present comprehensive genomic information in genetic and physical maps that cover all nine chromosomes. Based on this information we identified the proposed ancestral linkage groups of rosids and asterids within the sugar beet genome. We generated an extended genetic map that comprises 1127 single nucleotide polymorphism markers prepared from expressed sequence tags and bacterial artificial chromosome (BAC) end sequences. To construct a genome-wide physical map, we hybridized gene-derived oligomer probes against two BAC libraries with 9.5-fold cumulative coverage of the 758 Mbp genome. More than 2500 probes and clones were integrated both in genetic maps and the physical data. The final physical map encompasses 535 chromosomally anchored contigs that contains 8361 probes and 22 815 BAC clones. By using the gene order established with the physical map, we detected regions of synteny between sugar beet (order Caryophyllales) and rosid species that involves 1400-2700 genes in the sequenced genomes of Arabidopsis, poplar, grapevine, and cacao. The data suggest that Caryophyllales share the palaeohexaploid ancestor proposed for rosids and asterids. Taken together, we here provide extensive molecular resources for sugar beet and enable future high-resolution trait mapping, gene identification, and cross-referencing to regions sequenced in other plant species. © 2011 The Authors. The Plant Journal © 2011 Blackwell Publishing Ltd.

  2. Do echinoderm genomes measure up?

    Science.gov (United States)

    Cameron, R Andrew; Kudtarkar, Parul; Gordon, Susan M; Worley, Kim C; Gibbs, Richard A

    2015-08-01

    Echinoderm genome sequences are a corpus of useful information about a clade of animals that serve as research models in fields ranging from marine ecology to cell and developmental biology. Genomic information from echinoids has contributed to insights into the gene interactions that drive the developmental process at the molecular level. Such insights often rely heavily on genomic information and the kinds of questions that can be asked thus depend on the quality of the sequence information. Here we describe the history of echinoderm genomic sequence assembly and present details about the quality of the data obtained. All of the sequence information discussed here is posted on the echinoderm information web system, Echinobase.org. Copyright © 2015 Elsevier B.V. All rights reserved.

  3. Gene finding in novel genomes

    Directory of Open Access Journals (Sweden)

    Korf Ian

    2004-05-01

    Full Text Available Abstract Background Computational gene prediction continues to be an important problem, especially for genomes with little experimental data. Results I introduce the SNAP gene finder which has been designed to be easily adaptable to a variety of genomes. In novel genomes without an appropriate gene finder, I demonstrate that employing a foreign gene finder can produce highly inaccurate results, and that the most compatible parameters may not come from the nearest phylogenetic neighbor. I find that foreign gene finders are more usefully employed to bootstrap parameter estimation and that the resulting parameters can be highly accurate. Conclusion Since gene prediction is sensitive to species-specific parameters, every genome needs a dedicated gene finder.

  4. Genome engineering in human cells.

    Science.gov (United States)

    Song, Minjung; Kim, Young-Hoon; Kim, Jin-Soo; Kim, Hyongbum

    2014-01-01

    Genome editing in human cells is of great value in research, medicine, and biotechnology. Programmable nucleases including zinc-finger nucleases, transcription activator-like effector nucleases, and RNA-guided engineered nucleases recognize a specific target sequence and make a double-strand break at that site, which can result in gene disruption, gene insertion, gene correction, or chromosomal rearrangements. The target sequence complexities of these programmable nucleases are higher than 3.2 mega base pairs, the size of the haploid human genome. Here, we briefly introduce the structure of the human genome and the characteristics of each programmable nuclease, and review their applications in human cells including pluripotent stem cells. In addition, we discuss various delivery methods for nucleases, programmable nickases, and enrichment of gene-edited human cells, all of which facilitate efficient and precise genome editing in human cells.

  5. Genomic Resources for Cancer Epidemiology

    Science.gov (United States)

    This page provides links to research resources, complied by the Epidemiology and Genomics Research Program, that may be of interest to genetic epidemiologists conducting cancer research, but is not exhaustive.

  6. 2004 Structural, Function and Evolutionary Genomics

    Energy Technology Data Exchange (ETDEWEB)

    Douglas L. Brutlag Nancy Ryan Gray

    2005-03-23

    This Gordon conference will cover the areas of structural, functional and evolutionary genomics. It will take a systematic approach to genomics, examining the evolution of proteins, protein functional sites, protein-protein interactions, regulatory networks, and metabolic networks. Emphasis will be placed on what we can learn from comparative genomics and entire genomes and proteomes.

  7. Utilizing linkage disequilibrium information from Indian Genome ...

    Indian Academy of Sciences (India)

    Utilizing linkage disequilibrium information from Indian Genome. Variation Database for mapping mutations: SCA12 case study. SAMIRA BAHL1, IKHLAK AHMED2, THE INDIAN GENOME VARIATION CONSORTIUM3 and MITALI MUKERJI1. 1Functional Genomics Unit, Institute of Genomics and Integrative Biology (CSIR), ...

  8. Genomic Aspects of Research Involving Polyploid Plants

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Xiaohan [ORNL; Ye, Chuyu [ORNL; Tschaplinski, Timothy J [ORNL; Wullschleger, Stan D [ORNL; Tuskan, Gerald A [ORNL

    2011-01-01

    Almost all extant plant species have spontaneously doubled their genomes at least once in their evolutionary histories, resulting in polyploidy which provided a rich genomic resource for evolutionary processes. Moreover, superior polyploid clones have been created during the process of crop domestication. Polyploid plants generated by evolutionary processes and/or crop domestication have been the intentional or serendipitous focus of research dealing with the dynamics and consequences of genome evolution. One of the new trends in genomics research is to create synthetic polyploid plants which provide materials for studying the initial genomic changes/responses immediately after polyploid formation. Polyploid plants are also used in functional genomics research to study gene expression in a complex genomic background. In this review, we summarize the recent progress in genomics research involving ancient, young, and synthetic polyploid plants, with a focus on genome size evolution, genomics diversity, genomic rearrangement, genetic and epigenetic changes in duplicated genes, gene discovery, and comparative genomics. Implications on plant sciences including evolution, functional genomics, and plant breeding are presented. It is anticipated that polyploids will be a regular subject of genomics research in the foreseeable future as the rapid advances in DNA sequencing technology create unprecedented opportunities for discovering and monitoring genomic and transcriptomic changes in polyploid plants. The fast accumulation of knowledge on polyploid formation, maintenance, and divergence at whole-genome and subgenome levels will not only help plant biologists understand how plants have evolved and diversified, but also assist plant breeders in designing new strategies for crop improvement.

  9. Whole genome analysis of a Vietnamese trio

    Indian Academy of Sciences (India)

    2015-02-04

    Feb 4, 2015 ... The Ti/Tv ratios are 2.063, 2.064 and 2.063 in the child, father and mother genomes, respectively. The number of detected SNPs in each genome is comparable to those re- ported in other individual genome-wide studies such as. 3,132,608 SNPs in the first Japanese individual genome. (Fujimoto et al.

  10. Genomic instability and radiation effects

    International Nuclear Information System (INIS)

    Christian Streffer

    2007-01-01

    Complete text of publication follows. Cancer, genetic mutations and developmental abnormalities are apparently associated with an increased genomic instability. Such phenomena have been frequently shown in human cancer cells in vitro and in situ. It is also well-known that individuals with a genetic predisposition for cancer proneness, such as ataxia telangiectesia, Fanconi anaemia etc. demonstrate a general high genomic instability e.g. in peripheral lymphocytes before a cancer has developed. Analogous data have been found in mice which develop a specific congenital malformation which has a genetic background. Under these aspects it is of high interest that ionising radiation can increase the genomic instability of mammalian cells after exposures in vitro an in vivo. This phenomenon is expressed 20 to 40 cell cycles after the exposure e.g. by de novo chromosomal aberrations. Such effects have been observed with high and low LET radiation, high LET radiation is more efficient. With low LET radiation a good dose response is observed in the dose range 0.2 to 2.0 Gy, Recently it has been reported that senescence and genomic instability was induced in human fibroblasts after 1 mGy carbon ions (1 in 18 cells are hit), apparently bystander effects also occurred under these conditions. The instability has been shown with DNA damage, chromosomal aberrations, gene mutation and cell death. It is also transferred to the next generation of mice with respect to gene mutations, chromosomal aberrations and congenital malformations. Several mechanisms have been discussed. The involvement of telomeres has gained interest. Genomic instability seems to be induced by a general lesion to the whole genome. The transmission of one chromosome from an irradiated cell to an non-irradiated cell leads to genomic instability in the untreated cells. Genomic instability increases mutation rates in the affected cells in general. As radiation late effects (cancer, gene mutations and congenital

  11. IS4 family goes genomic

    Directory of Open Access Journals (Sweden)

    Mahillon Jacques

    2008-01-01

    Full Text Available Abstract Background Insertion sequences (ISs are small, mobile DNA entities able to expand in prokaryotic genomes and trigger important rearrangements. To understand their role in evolution, accurate IS taxonomy is essential. The IS4 family is composed of ~70 elements and, like some other families, displays extremely elevated levels of internal divergence impeding its classification. The increasing availability of complete genome sequences provides a valuable source for the discovery of additional IS4 elements. In this study, this genomic database was used to update the structural and functional definition of the IS4 family. Results A total of 227 IS4-related sequences were collected among more than 500 sequenced bacterial and archaeal genomes, representing more than a three fold increase of the initial inventory. A clear division into seven coherent subgroups was discovered as well as three emerging families, which displayed distinct structural and functional properties. The IS4 family was sporadically present in 17 % of analyzed genomes, with most of them displaying single or a small number of IS4 elements. Significant expansions were detected only in some pathogens as well as among certain extremophiles, suggesting the probable involvement of some elements in bacterial and archaeal adaptation and/or evolution. Finally, it should be noted that some IS4 subgroups and two emerging families occurred preferentially in specific phyla or exclusively inside a specific genus. Conclusion The present taxonomic update of IS4 and emerging families will facilitate the classification of future elements as they arise from ongoing genome sequencing. Their narrow genomic impact and the existence of both IS-poor and IS-rich thriving prokaryotes suggested that these families, and probably ISs in general, are occasionally used as a tool for genome flexibility and evolution, rather than just representing self sustaining DNA entities.

  12. GOBASE: an organelle genome database

    OpenAIRE

    O?Brien, Emmet A.; Zhang, Yue; Wang, Eric; Marie, Veronique; Badejoko, Wole; Lang, B. Franz; Burger, Gertraud

    2008-01-01

    The organelle genome database GOBASE, now in its 21st release (June 2008), contains all published mitochondrion-encoded sequences (?913 000) and chloroplast-encoded sequences (?250 000) from a wide range of eukaryotic taxa. For all sequences, information on related genes, exons, introns, gene products and taxonomy is available, as well as selected genome maps and RNA secondary structures. Recent major enhancements to database functionality include: (i) addition of an interface for RNA editing...

  13. Functional genomics of probiotic Lactobacilli.

    Science.gov (United States)

    Klaenhammer, Todd R; Altermann, Eric; Pfeiler, Erika; Buck, Brock Logan; Goh, Yong-Jun; O'Flaherty, Sarah; Barrangou, Rodolphe; Duong, Tri

    2008-09-01

    Lactic acid bacteria (LAB) have been used in fermentation processes for millennia. Recent applications such as the use of living cultures as probiotics have significantly increased industrial interest. Related bacterial strains can differ significantly in their genotype and phenotype, and features from one bacterial strain or species cannot necessarily be applied to a related one. These strain or family-specific differences often represent unique and applicable traits. Since 2002, the complete genomes of 13 probiotic LABs have been published. The presentation will discuss these genomes and highlight probiotic traits that are predicted, or functionally linked to genetic content. We have conducted a comparative genomic analysis of 4 completely sequenced Lactobacillus strains versus 25 lactic acid bacterial genomes present in the public database at the time of analysis. Using Differential Blast Analysis, each genome is compared with 3 other Lactobacillus and 25 other LAB genomes. Differential Blast Analysis highlighted strain-specific genes that were not represented in any other LAB used in this analysis and also identified group-specific genes shared within lactobacilli. Lactobacillus-specific genes include mucus-binding proteins involved in cell-adhesion and several transport systems for carbohydrates and amino acids. Comparative genomic analysis has identified gene targets in Lactobacillus acidophilus for functional analysis, including adhesion to mucin and intestinal epithelial cells, acid tolerance, bile tolerance, and quorum sensing. Whole genome transcriptional profiling of L. acidophilus, and isogenic mutants thereof, has revealed the impact of varying conditions (pH, bile, carbohydrates) and food matrices on the expression of genes important to probiotic-linked mechanisms.

  14. Population Genomics of Paramecium Species.

    Science.gov (United States)

    Johri, Parul; Krenek, Sascha; Marinov, Georgi K; Doak, Thomas G; Berendonk, Thomas U; Lynch, Michael

    2017-05-01

    Population-genomic analyses are essential to understanding factors shaping genomic variation and lineage-specific sequence constraints. The dearth of such analyses for unicellular eukaryotes prompted us to assess genomic variation in Paramecium, one of the most well-studied ciliate genera. The Paramecium aurelia complex consists of ∼15 morphologically indistinguishable species that diverged subsequent to two rounds of whole-genome duplications (WGDs, as long as 320 MYA) and possess extremely streamlined genomes. We examine patterns of both nuclear and mitochondrial polymorphism, by sequencing whole genomes of 10-13 worldwide isolates of each of three species belonging to the P. aurelia complex: P. tetraurelia, P. biaurelia, P. sexaurelia, as well as two outgroup species that do not share the WGDs: P. caudatum and P. multimicronucleatum. An apparent absence of global geographic population structure suggests continuous or recent dispersal of Paramecium over long distances. Intergenic regions are highly constrained relative to coding sequences, especially in P. caudatum and P. multimicronucleatum that have shorter intergenic distances. Sequence diversity and divergence are reduced up to ∼100-150 bp both upstream and downstream of genes, suggesting strong constraints imposed by the presence of densely packed regulatory modules. In addition, comparison of sequence variation at non-synonymous and synonymous sites suggests similar recent selective pressures on paralogs within and orthologs across the deeply diverging species. This study presents the first genome-wide population-genomic analysis in ciliates and provides a valuable resource for future studies in evolutionary and functional genetics in Paramecium. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  15. Genome Exploitation and Bioinformatics Tools

    Science.gov (United States)

    de Jong, Anne; van Heel, Auke J.; Kuipers, Oscar P.

    Bioinformatic tools can greatly improve the efficiency of bacteriocin screening efforts by limiting the amount of strains. Different classes of bacteriocins can be detected in genomes by looking at different features. Finding small bacteriocins can be especially challenging due to low homology and because small open reading frames (ORFs) are often omitted from annotations. In this chapter, several bioinformatic tools/strategies to identify bacteriocins in genomes are discussed.

  16. Plague in the genomic area.

    Science.gov (United States)

    Drancourt, M

    2012-03-01

    With plague being not only a subject of interest for historians, but still a disease of public health concern in several countries, mainly in Africa, there were hopes that analyses of the Yersinia pestis genomes would put an end to this deadly epidemic pathogen. Genomics revealed that Y. pestis isolates evolved from Yersinia pseudotuberculosis in Central Asia some millennia ago, after the acquisition of two Y. pestis-specific plasmids balanced genomic reduction parallel with the expansion of insertion sequences, illustrating the modern concept that, except for the acquisition of plasmid-borne toxin-encoding genes, the increased virulence of Y. pestis resulted from gene loss rather than gene acquisition. The telluric persistence of Y. pestis reminds us of this close relationship, and matters in terms of plague epidemiology. Whereas biotype Orientalis isolates spread worldwide, the Antiqua and Medievalis isolates showed more limited expansion. In addition to animal ectoparasites, human ectoparasites such as the body louse may have participated in this expansion and in devastating historical epidemics. The recent analysis of a Black Death genome indicated that it was more closely related to the Orientalis branch than to the Medievalis branch. Modern Y. pestis isolates grossly exhibit the same gene content, but still undergo micro-evolution in geographically limited areas by differing in the genome architecture, owing to inversions near insertion sequences and the stabilization of the YpfPhi prophage in Orientalis biotype isolates. Genomics have provided several new molecular tools for the genotyping and phylogeographical tracing of isolates and description of plague foci. However, genomics and post-genomics approaches have not yet provided new tools for the prevention, diagnosis and management of plague patients and the plague epidemics still raging in some sub-Saharan countries. © 2012 The Author. Clinical Microbiology and Infection © 2012 European Society of

  17. The fishes of Genome 10K

    KAUST Repository

    Bernardi, Giacomo

    2012-09-01

    The Genome 10K project aims to sequence the genomes of 10,000 vertebrates, representing approximately one genome for each vertebrate genus. Since fishes (cartilaginous fishes, ray-finned fishes and lobe-finned fishes) represent more than 50% of extant vertebrates, it is planned to target 4,000 fish genomes. At present, nearly 60 fish genomes are being sequenced at various public funded labs, and under a Genome 10K and BGI pilot project. An additional 100 fishes have been identified for sequencing in the next phase of Genome 10K project. © 2012 Elsevier B.V.

  18. Packaging the fly genome: domains and dynamics.

    Science.gov (United States)

    White, Rob

    2012-09-01

    Two independent genomic approaches have recently converged to provide insight into the domain organization of the Drosophila genome. Genome-wide mapping of chromosomal proteins and histone modifications has generated detailed maps of the Drosophila chromatin landscape and has led to the identification of a number of different chromatin states and their distribution in domains across the genome. A remarkably similar domain organization is derived from whole genome mapping of chromatin interactions that reveals the segmentation of the genome into structural domains. This review focuses on our current understanding of this domain architecture which provides a foundation for our understanding of the link between chromatin organization and the dynamic activity of the genome.

  19. Mutational Dynamics of Aroid Chloroplast Genomes

    Science.gov (United States)

    Ahmed, Ibrar; Biggs, Patrick J.; Matthews, Peter J.; Collins, Lesley J.; Hendy, Michael D.; Lockhart, Peter J.

    2012-01-01

    A characteristic feature of eukaryote and prokaryote genomes is the co-occurrence of nucleotide substitution and insertion/deletion (indel) mutations. Although similar observations have also been made for chloroplast DNA, genome-wide associations have not been reported. We determined the chloroplast genome sequences for two morphotypes of taro (Colocasia esculenta; family Araceae) and compared these with four publicly available aroid chloroplast genomes. Here, we report the extent of genome-wide association between direct and inverted repeats, indels, and substitutions in these aroid chloroplast genomes. We suggest that alternative but not mutually exclusive hypotheses explain the mutational dynamics of chloroplast genome evolution. PMID:23204304

  20. Rat Genome and Model Resources.

    Science.gov (United States)

    Shimoyama, Mary; Smith, Jennifer R; Bryda, Elizabeth; Kuramoto, Takashi; Saba, Laura; Dwinell, Melinda

    2017-07-01

    Rats remain a major model for studying disease mechanisms and discovery, validation, and testing of new compounds to improve human health. The rat's value continues to grow as indicated by the more than 1.4 million publications (second to human) at PubMed documenting important discoveries using this model. Advanced sequencing technologies, genome modification techniques, and the development of embryonic stem cell protocols ensure the rat remains an important mammalian model for disease studies. The 2004 release of the reference genome has been followed by the production of complete genomes for more than two dozen individual strains utilizing NextGen sequencing technologies; their analyses have identified over 80 million variants. This explosion in genomic data has been accompanied by the ability to selectively edit the rat genome, leading to hundreds of new strains through multiple technologies. A number of resources have been developed to provide investigators with access to precision rat models, comprehensive datasets, and sophisticated software tools necessary for their research. Those profiled here include the Rat Genome Database, PhenoGen, Gene Editing Rat Resource Center, Rat Resource and Research Center, and the National BioResource Project for the Rat in Japan. © The Author 2017. Published by Oxford University Press.

  1. Evolutionary genomics of environmental pollution.

    Science.gov (United States)

    Whitehead, Andrew

    2014-01-01

    Chemical toxins have been a persistent source of evolutionary challenges throughout the history of life, and deep within the genomic storehouse of evolutionary history lay ancient adaptations to diverse chemical poisons. However, the rate of change of contemporary environments mediated by human-introduced pollutants is rapidly screening this storehouse and severely testing the adaptive potential of many species. In this chapter, we briefly review the deep history of evolutionary adaptation to environmental toxins, and then proceed to describe the attributes of stressors and populations that may facilitate contemporary adaptation to pollutants introduced by humans. We highlight that phenotypes derived to enable persistence in polluted habitats may be multi-dimensional, requiring global genome-scale tools and approaches to uncover their mechanistic basis, and include examples of recent progress in the field. The modern tools of genomics offer promise for discovering how pollutants interact with genomes on physiological timescales, and also for discovering what genomic attributes of populations may enable resistance to pollutants over evolutionary timescales. Through integration of these sophisticated genomics tools and approaches with an understanding of the deep historical forces that shaped current populations, a more mature understanding of the mechanistic basis of contemporary ecological-evolutionary dynamics should emerge.

  2. The dynamic genome of Hydra.

    Science.gov (United States)

    Chapman, Jarrod A; Kirkness, Ewen F; Simakov, Oleg; Hampson, Steven E; Mitros, Therese; Weinmaier, Thomas; Rattei, Thomas; Balasubramanian, Prakash G; Borman, Jon; Busam, Dana; Disbennett, Kathryn; Pfannkoch, Cynthia; Sumin, Nadezhda; Sutton, Granger G; Viswanathan, Lakshmi Devi; Walenz, Brian; Goodstein, David M; Hellsten, Uffe; Kawashima, Takeshi; Prochnik, Simon E; Putnam, Nicholas H; Shu, Shengquiang; Blumberg, Bruce; Dana, Catherine E; Gee, Lydia; Kibler, Dennis F; Law, Lee; Lindgens, Dirk; Martinez, Daniel E; Peng, Jisong; Wigge, Philip A; Bertulat, Bianca; Guder, Corina; Nakamura, Yukio; Ozbek, Suat; Watanabe, Hiroshi; Khalturin, Konstantin; Hemmrich, Georg; Franke, André; Augustin, René; Fraune, Sebastian; Hayakawa, Eisuke; Hayakawa, Shiho; Hirose, Mamiko; Hwang, Jung Shan; Ikeo, Kazuho; Nishimiya-Fujisawa, Chiemi; Ogura, Atshushi; Takahashi, Toshio; Steinmetz, Patrick R H; Zhang, Xiaoming; Aufschnaiter, Roland; Eder, Marie-Kristin; Gorny, Anne-Kathrin; Salvenmoser, Willi; Heimberg, Alysha M; Wheeler, Benjamin M; Peterson, Kevin J; Böttger, Angelika; Tischler, Patrick; Wolf, Alexander; Gojobori, Takashi; Remington, Karin A; Strausberg, Robert L; Venter, J Craig; Technau, Ulrich; Hobmayer, Bert; Bosch, Thomas C G; Holstein, Thomas W; Fujisawa, Toshitaka; Bode, Hans R; David, Charles N; Rokhsar, Daniel S; Steele, Robert E

    2010-03-25

    The freshwater cnidarian Hydra was first described in 1702 and has been the object of study for 300 years. Experimental studies of Hydra between 1736 and 1744 culminated in the discovery of asexual reproduction of an animal by budding, the first description of regeneration in an animal, and successful transplantation of tissue between animals. Today, Hydra is an important model for studies of axial patterning, stem cell biology and regeneration. Here we report the genome of Hydra magnipapillata and compare it to the genomes of the anthozoan Nematostella vectensis and other animals. The Hydra genome has been shaped by bursts of transposable element expansion, horizontal gene transfer, trans-splicing, and simplification of gene structure and gene content that parallel simplification of the Hydra life cycle. We also report the sequence of the genome of a novel bacterium stably associated with H. magnipapillata. Comparisons of the Hydra genome to the genomes of other animals shed light on the evolution of epithelia, contractile tissues, developmentally regulated transcription factors, the Spemann-Mangold organizer, pluripotency genes and the neuromuscular junction.

  3. Human genomics: implications for health.

    Science.gov (United States)

    Wasi, P

    1997-01-01

    Human genome research which tries to map and sequence all the 3 billion nucleotides in the entire DNA is progressing rapidly. Completion of the human genome sequencing is expected before the year 2005. Human genes, totalling 50,000-100,000, will be identified, allowing the complete set of proteins--'the proteome' to be known. This together with genomic research in other species will lead to complete understanding of life at the molecular level and also its evolutionary history of 3,500 million years. Genomics will bring about a revolution in biology and health, because it is equivalent to having a 'Biological Periodic Table' which is a foundation for understanding life, health, disease and for deriving of new tools for diagnosis, treatment, prognosis and prevention. Human genomics will give rise to Predictive--Preventive Medicine and Precision Medicine. It will have profound social implications. Preparation for the future is needed for societies to cope with and make proper use of the tremendous changes to be brought about by genomics.

  4. A Genome-Wide Perspective on Metabolism

    DEFF Research Database (Denmark)

    Rauch, Alexander; Mandrup, Susanne

    2015-01-01

    number of technologies that can be used to obtain genome-wide insight into how genomes are reprogrammed during development and in response to specific external signals. By applying such technologies, we have begun to reveal the cross-talk between metabolism and the genome, i.e., how genomes...... are reprogrammed in response to metabolites, and how the regulation of metabolic networks is coordinated at the genomic level....

  5. HGVA: the Human Genome Variation Archive

    OpenAIRE

    Lopez, Javier; Coll, Jacobo; Haimel, Matthias; Kandasamy, Swaathi; Tarraga, Joaquin; Furio-Tari, Pedro; Bari, Wasim; Bleda, Marta; Rueda, Antonio; Gr?f, Stefan; Rendon, Augusto; Dopazo, Joaquin; Medina, Ignacio

    2017-01-01

    Abstract High-profile genomic variation projects like the 1000 Genomes project or the Exome Aggregation Consortium, are generating a wealth of human genomic variation knowledge which can be used as an essential reference for identifying disease-causing genotypes. However, accessing these data, contrasting the various studies and integrating those data in downstream analyses remains cumbersome. The Human Genome Variation Archive (HGVA) tackles these challenges and facilitates access to genomic...

  6. Genomics of ankylosing spondylitis.

    Science.gov (United States)

    Thomas, Gethin P; Brown, Matthew A

    2010-09-01

    Ankylosing spondylitis (AS) is the prototypic and most prevalent and debilitating spondyloarthropathy, a group of arthritides where the spine and pelvis are specifically targeted. Unlike many other forms of arthritis in which joint damage is mediated through tissue destruction, in AS uncontrolled bone formation occurs, frequently resulting in joint fusion and consequently significant disability. It is estimated that there are 2.4 million spondyloarthritis sufferers in the U.S., twice as many as rheumatoid arthritis. The pathogenesis of AS is very poorly understood and both genetics and gene expression profiling approaches have been utilized to elucidate the underlying mechanisms and pathways that drive the disease. Using powerful genome-wide association study approaches a number of candidate genes have been found to be associated with AS. However, although such approaches can identify genes that can contribute to the disease process, they do not inform us of the actual changes in gene/cell activity at any point in the disease process. Expression profiling allows us to take a "snapshot" of cellular activity and what gene activity changes are underlying those changes. A number of expression profiling studies have been undertaken in AS, looking at both circulating cells and tissues from affected joints. The results to date have been somewhat disappointing with little consensus on gene activity changes due to the low power of the studies undertaken. Some more recent better powered studies have identified diagnostic expression profiles that do point to a possible role for expression profiling in early AS diagnosis. Future studies will require collaborative approaches to target specific disease stages and sites with larger numbers of samples.

  7. Whole-genome cartography of p53 response elements ranked on transactivation potential.

    Science.gov (United States)

    Tebaldi, Toma; Zaccara, Sara; Alessandrini, Federica; Bisio, Alessandra; Ciribilli, Yari; Inga, Alberto

    2015-06-17

    Many recent studies using ChIP-seq approaches cross-referenced to trascriptome data and also to potentially unbiased in vitro DNA binding selection experiments are detailing with increasing precision the p53-directed gene regulatory network that, nevertheless, is still expanding. However, most experiments have been conducted in established cell lines subjected to specific p53-inducing stimuli, both factors potentially biasing the results. We developed p53retriever, a pattern search algorithm that maps p53 response elements (REs) and ranks them according to predicted transactivation potentials in five classes. Besides canonical, full site REs, we developed specific pattern searches for non-canonical half sites and 3/4 sites and show that they can mediate p53-dependent responsiveness of associated coding sequences. Using ENCODE data, we also mapped p53 REs in about 44,000 distant enhancers and identified a 16-fold enrichment for high activity REs within those sites in the comparison with genomic regions near transcriptional start sites (TSS). Predictions from our pattern search were cross-referenced to ChIP-seq, ChIP-exo, expression, and various literature data sources. Based on the mapping of predicted functional REs near TSS, we examined expression changes of thirteen genes as a function of different p53-inducing conditions, providing further evidence for PDE2A, GAS6, E2F7, APOBEC3H, KCTD1, TRIM32, DICER, HRAS, KITLG and TGFA p53-dependent regulation, while MAP2K3, DNAJA1 and potentially YAP1 were identified as new direct p53 target genes. We provide a comprehensive annotation of canonical and non-canonical p53 REs in the human genome, ranked on predicted transactivation potential. We also establish or corroborate direct p53 transcriptional control of thirteen genes. The entire list of identified and functionally classified p53 REs near all UCSC-annotated genes and within ENCODE mapped enhancer elements is provided. Our approach is distinct from, and complementary

  8. A dictionary based informational genome analysis

    Directory of Open Access Journals (Sweden)

    Castellini Alberto

    2012-09-01

    Full Text Available Abstract Background In the post-genomic era several methods of computational genomics are emerging to understand how the whole information is structured within genomes. Literature of last five years accounts for several alignment-free methods, arisen as alternative metrics for dissimilarity of biological sequences. Among the others, recent approaches are based on empirical frequencies of DNA k-mers in whole genomes. Results Any set of words (factors occurring in a genome provides a genomic dictionary. About sixty genomes were analyzed by means of informational indexes based on genomic dictionaries, where a systemic view replaces a local sequence analysis. A software prototype applying a methodology here outlined carried out some computations on genomic data. We computed informational indexes, built the genomic dictionaries with different sizes, along with frequency distributions. The software performed three main tasks: computation of informational indexes, storage of these in a database, index analysis and visualization. The validation was done by investigating genomes of various organisms. A systematic analysis of genomic repeats of several lengths, which is of vivid interest in biology (for example to compute excessively represented functional sequences, such as promoters, was discussed, and suggested a method to define synthetic genetic networks. Conclusions We introduced a methodology based on dictionaries, and an efficient motif-finding software application for comparative genomics. This approach could be extended along many investigation lines, namely exported in other contexts of computational genomics, as a basis for discrimination of genomic pathologies.

  9. The Genomic Code: Genome Evolution and Potential Applications

    KAUST Repository

    Bernardi, Giorgio

    2016-01-25

    The genome of metazoans is organized according to a genomic code which comprises three laws: 1) Compositional correlations hold between contiguous coding and non-coding sequences, as well as among the three codon positions of protein-coding genes; these correlations are the consequence of the fact that the genomes under consideration consist of fairly homogeneous, long (≥200Kb) sequences, the isochores; 2) Although isochores are defined on the basis of purely compositional properties, GC levels of isochores are correlated with all tested structural and functional properties of the genome; 3) GC levels of isochores are correlated with chromosome architecture from interphase to metaphase; in the case of interphase the correlation concerns isochores and the three-dimensional “topological associated domains” (TADs); in the case of mitotic chromosomes, the correlation concerns isochores and chromosomal bands. Finally, the genomic code is the fourth and last pillar of molecular biology, the first three pillars being 1) the double helix structure of DNA; 2) the regulation of gene expression in prokaryotes; and 3) the genetic code.

  10. Genome sequencing and population genomics in non-model organisms.

    Science.gov (United States)

    Ellegren, Hans

    2014-01-01

    High-throughput sequencing technologies are revolutionizing the life sciences. The past 12 months have seen a burst of genome sequences from non-model organisms, in each case representing a fundamental source of data of significant importance to biological research. This has bearing on several aspects of evolutionary biology, and we are now beginning to see patterns emerging from these studies. These include significant heterogeneity in the rate of recombination that affects adaptive evolution and base composition, the role of population size in adaptive evolution, and the importance of expansion of gene families in lineage-specific adaptation. Moreover, resequencing of population samples (population genomics) has enabled the identification of the genetic basis of critical phenotypes and cast light on the landscape of genomic divergence during speciation. Copyright © 2013 Elsevier Ltd. All rights reserved.

  11. Human Genome Education Program

    Energy Technology Data Exchange (ETDEWEB)

    Richard Myers; Lane Conn

    2000-05-01

    The funds from the DOE Human Genome Program, for the project period 2/1/96 through 1/31/98, have provided major support for the curriculum development and field testing efforts for two high school level instructional units: Unit 1, ''Exploring Genetic Conditions: Genes, Culture and Choices''; and Unit 2, ''DNA Snapshots: Peaking at Your DNA''. In the original proposal, they requested DOE support for the partial salary and benefits of a Field Test Coordinator position to: (1) complete the field testing and revision of two high school curriculum units, and (2) initiate the education of teachers using these units. During the project period of this two-year DOE grant, a part-time Field-Test Coordinator was hired (Ms. Geraldine Horsma) and significant progress has been made in both of the original proposal objectives. Field testing for Unit 1 has occurred in over 12 schools (local and non-local sites with diverse student populations). Field testing for Unit 2 has occurred in over 15 schools (local and non-local sites) and will continue in 12-15 schools during the 96-97 school year. For both curricula, field-test sites and site teachers were selected for their interest in genetics education and in hands-on science education. Many of the site teachers had no previous experience with HGEP or the unit under development. Both of these first-year biology curriculum units, which contain genetics, biotechnology, societal, ethical and cultural issues related to HGP, are being implemented in many local and non-local schools (SF Bay Area, Southern California, Nebraska, Hawaii, and Texas) and in programs for teachers. These units will reach over 10,000 students in the SF Bay Area and continues to receive support from local corporate and private philanthropic organizations. Although HGEP unit development is nearing completion for both units, data is still being gathered and analyzed on unit effectiveness and student learning. The final field

  12. Allele coding in genomic evaluation

    Directory of Open Access Journals (Sweden)

    Christensen Ole F

    2011-06-01

    Full Text Available Abstract Background Genomic data are used in animal breeding to assist genetic evaluation. Several models to estimate genomic breeding values have been studied. In general, two approaches have been used. One approach estimates the marker effects first and then, genomic breeding values are obtained by summing marker effects. In the second approach, genomic breeding values are estimated directly using an equivalent model with a genomic relationship matrix. Allele coding is the method chosen to assign values to the regression coefficients in the statistical model. A common allele coding is zero for the homozygous genotype of the first allele, one for the heterozygote, and two for the homozygous genotype for the other allele. Another common allele coding changes these regression coefficients by subtracting a value from each marker such that the mean of regression coefficients is zero within each marker. We call this centered allele coding. This study considered effects of different allele coding methods on inference. Both marker-based and equivalent models were considered, and restricted maximum likelihood and Bayesian methods were used in inference. Results Theoretical derivations showed that parameter estimates and estimated marker effects in marker-based models are the same irrespective of the allele coding, provided that the model has a fixed general mean. For the equivalent models, the same results hold, even though different allele coding methods lead to different genomic relationship matrices. Calculated genomic breeding values are independent of allele coding when the estimate of the general mean is included into the values. Reliabilities of estimated genomic breeding values calculated using elements of the inverse of the coefficient matrix depend on the allele coding because different allele coding methods imply different models. Finally, allele coding affects the mixing of Markov chain Monte Carlo algorithms, with the centered coding being

  13. Genomic selection in maritime pine.

    Science.gov (United States)

    Isik, Fikret; Bartholomé, Jérôme; Farjat, Alfredo; Chancerel, Emilie; Raffin, Annie; Sanchez, Leopoldo; Plomion, Christophe; Bouffier, Laurent

    2016-01-01

    A two-generation maritime pine (Pinus pinaster Ait.) breeding population (n=661) was genotyped using 2500 SNP markers. The extent of linkage disequilibrium and utility of genomic selection for growth and stem straightness improvement were investigated. The overall intra-chromosomal linkage disequilibrium was r(2)=0.01. Linkage disequilibrium corrected for genomic relationships derived from markers was smaller (rV(2)=0.006). Genomic BLUP, Bayesian ridge regression and Bayesian LASSO regression statistical models were used to obtain genomic estimated breeding values. Two validation methods (random sampling 50% of the population and 10% of the progeny generation as validation sets) were used with 100 replications. The average predictive ability across statistical models and validation methods was about 0.49 for stem sweep, and 0.47 and 0.43 for total height and tree diameter, respectively. The sensitivity analysis suggested that prior densities (variance explained by markers) had little or no discernible effect on posterior means (residual variance) in Bayesian prediction models. Sampling from the progeny generation for model validation increased the predictive ability of markers for tree diameter and stem sweep but not for total height. The results are promising despite low linkage disequilibrium and low marker coverage of the genome (∼1.39 markers/cM). Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  14. The genome of Chenopodium quinoa

    KAUST Repository

    Jarvis, David Erwin

    2017-02-08

    Chenopodium quinoa (quinoa) is a highly nutritious grain identified as an important crop to improve world food security. Unfortunately, few resources are available to facilitate its genetic improvement. Here we report the assembly of a high-quality, chromosome-scale reference genome sequence for quinoa, which was produced using single-molecule real-time sequencing in combination with optical, chromosome-contact and genetic maps. We also report the sequencing of two diploids from the ancestral gene pools of quinoa, which enables the identification of sub-genomes in quinoa, and reduced-coverage genome sequences for 22 other samples of the allotetraploid goosefoot complex. The genome sequence facilitated the identification of the transcription factor likely to control the production of anti-nutritional triterpenoid saponins found in quinoa seeds, including a mutation that appears to cause alternative splicing and a premature stop codon in sweet quinoa strains. These genomic resources are an important first step towards the genetic improvement of quinoa.

  15. Comparative genomics for biodiversity conservation

    Directory of Open Access Journals (Sweden)

    Catherine E. Grueber

    2015-01-01

    Full Text Available Genomic approaches are gathering momentum in biology and emerging opportunities lie in the creative use of comparative molecular methods for revealing the processes that influence diversity of wildlife. However, few comparative genomic studies are performed with explicit and specific objectives to aid conservation of wild populations. Here I provide a brief overview of comparative genomic approaches that offer specific benefits to biodiversity conservation. Because conservation examples are few, I draw on research from other areas to demonstrate how comparing genomic data across taxa may be used to inform the characterisation of conservation units and studies of hybridisation, as well as studies that provide conservation outcomes from a better understanding of the drivers of divergence. A comparative approach can also provide valuable insight into the threatening processes that impact rare species, such as emerging diseases and their management in conservation. In addition to these opportunities, I note areas where additional research is warranted. Overall, comparing and contrasting the genomic composition of threatened and other species provide several useful tools for helping to preserve the molecular biodiversity of the global ecosystem.

  16. Genomic disorders on chromosome 22.

    Science.gov (United States)

    Yu, Shihui; Graf, William D; Shprintzen, Robert J

    2012-12-01

    Chromosome 22, the first human chromosome to be completely sequenced, is prone to genomic alterations. Copy-number variants (CNVs) are common because of an enrichment of low-copy repeat sequences that precipitate a high frequency of nonallelic homologous misalignments and unequal recombination during meiosis. Among these is one of the most common multiple anomaly syndromes in humans and the most common microdeletion syndrome, velocardiofacial syndrome (VCFS), also known as 22q11.2 deletion syndrome and DiGeorge syndrome. This review will focus on the recent literature dealing with both the molecular and clinical aspects of chromosome 22 genomic variations. Although the literature covering this area is expansive, the majority is descriptive or analytical of the problems presented by these genomic disorders, and there is little evidence of translational research including treatment outcomes. With the increased use of microarray analysis in both research and clinical practice, variations in CNVs are becoming elucidated. Genomic analysis continues to characterize genes and gene effect. Research on the COMT gene continues to yield interesting findings, including a possible sex-mediated effect because of its regulatory role with estrogen. There is a small amount of treatment outcome data relevant to neuropsychiatric disorders in VCFS, but based on small samples and short-term follow-up. Although hundreds of studies in the past year have focused on genomic disorders of chromosome 22, little progress has been made in the implementation of translational research, even for more common disorders including VCFS.

  17. The genome of Chenopodium quinoa.

    Science.gov (United States)

    Jarvis, David E; Ho, Yung Shwen; Lightfoot, Damien J; Schmöckel, Sandra M; Li, Bo; Borm, Theo J A; Ohyanagi, Hajime; Mineta, Katsuhiko; Michell, Craig T; Saber, Noha; Kharbatia, Najeh M; Rupper, Ryan R; Sharp, Aaron R; Dally, Nadine; Boughton, Berin A; Woo, Yong H; Gao, Ge; Schijlen, Elio G W M; Guo, Xiujie; Momin, Afaque A; Negrão, Sónia; Al-Babili, Salim; Gehring, Christoph; Roessner, Ute; Jung, Christian; Murphy, Kevin; Arold, Stefan T; Gojobori, Takashi; Linden, C Gerard van der; van Loo, Eibertus N; Jellen, Eric N; Maughan, Peter J; Tester, Mark

    2017-02-16

    Chenopodium quinoa (quinoa) is a highly nutritious grain identified as an important crop to improve world food security. Unfortunately, few resources are available to facilitate its genetic improvement. Here we report the assembly of a high-quality, chromosome-scale reference genome sequence for quinoa, which was produced using single-molecule real-time sequencing in combination with optical, chromosome-contact and genetic maps. We also report the sequencing of two diploids from the ancestral gene pools of quinoa, which enables the identification of sub-genomes in quinoa, and reduced-coverage genome sequences for 22 other samples of the allotetraploid goosefoot complex. The genome sequence facilitated the identification of the transcription factor likely to control the production of anti-nutritional triterpenoid saponins found in quinoa seeds, including a mutation that appears to cause alternative splicing and a premature stop codon in sweet quinoa strains. These genomic resources are an important first step towards the genetic improvement of quinoa.

  18. Manipulating duckweed through genome duplication.

    Science.gov (United States)

    Vunsh, R; Heinig, U; Malitsky, S; Aharoni, A; Avidov, A; Lerner, A; Edelman, M

    2015-01-01

    Significant inter- and intraspecific genetic variation exists in duckweed, thus the potential for genome plasticity and manipulation is high. Polyploidy is recognised as a major mechanism of adaptation and speciation in plants. We produced several genome-duplicated lines of Landoltia punctata (Spirodela oligorrhiza) from both whole plants and regenerating explants using a colchicine-based cocktail. These lines stably maintained an enlarged frond and root morphology. DNA ploidy levels determined by florescence-activated cell sorting indicated genome duplication. Line A4 was analysed after 75 biomass doublings. Frond area, fresh and dry weights, rhizoid number and length were significantly increased versus wild type, while the growth rate was unchanged. This resulted in accumulation of biomass 17-20% faster in the A4 plants. We sought to determine if specific differences in gene products are found in the genome duplicated lines. Non-targeted ultra performance LC-quadrupole time of flight mass spectrometry was employed to compare some of the lines and the wild type to seek identification of up-regulated metabolites. We putatively identified differential metabolites in Line A65 as caffeoyl hexoses. The combination of directed genome duplication and metabolic profiling might offer a path for producing stable gene expression, leading to altered production of secondary metabolites. © 2014 German Botanical Society and The Royal Botanical Society of the Netherlands.

  19. Genomic composition factors affect codon usage in porcine genome

    DEFF Research Database (Denmark)

    Khobondo, J O; Okeno, Tobias O; Kahi, A K

    2015-01-01

    The objective of the study was to determine the codon usage bias in the porcine genome and decipher its determinants. To investigate the underlying mechanisms of codon bias, the coding sequence (CDS) from the swine reference sequence (ssc10.2) was extracted using Biomart. An in house built Perl...... script was used to derive various genomic traits and codon indices. Analysis was done using R statistical package, and correlations and multivariate regressions were performed. We report the existence of codon usage bias that might suggest existence of weak translational selection. The codon bias...

  20. A physical map of the human genome

    Energy Technology Data Exchange (ETDEWEB)

    McPherson, J.D.; Marra, M.; Hillier, L.; Waterston, R.H.; Chinwalla, A.; Wallis, J.; Sekhon, M.; Wylie, K.; Mardis, E.R.; Wilson, R.K.; Fulton, R.; Kucaba, T.A.; Wagner-McPherson, C.; Barbazuk, W.B.; Gregory, S.G.; Humphray, S.J.; French, L.; Evans, R.S.; Bethel, G.; Whittaker, A.; Holden, J.L.; McCann, O.T.; Dunham, A.; Soderlund, C.; Scott, C.E.; Bentley, D.R.; Schuler, G.; Chen, H.-C.; Jang, W.; Green, E.D.; Idol, J.R.; Maduro, V.V. Braden; Montgomery, K.T.; Lee, E.; Miller, A.; Emerling, S.; Kucherlapati; Gibbs, R.; Scherer, S.; Gorrell, J.H.; Sodergren, E.; Clerc-Blankenburg, K.; Tabor, P.; Naylor, S.; Garcia, D.; de Jong, P.J.; Catanese, J.J.; Nowak, N.; Osoegawa, K.; Qin, S.; Rowen, L.; Madan, A.; Dors, M.; Hood, L.; Trask, B.; Friedman, C.; Massa, H.; Cheung, V.G.; Kirsch, I.R.; Reid, T.; Yonescu, R.; Weissenbach, J.; Bruls, T.; Heilig, R.; Branscomb, E.; Olsen, A.; Doggett, N.; Cheng, J.F.; Hawkins, T.; Myers, R.M.; Shang, J.; Ramirez, L.; Schmutz, J.; Velasquez, O.; Dixon, K.; Stone, N.E.; Cox, D.R.; Haussler, D.; Kent, W.J.; Furey, T.; Rogic, S.; Kennedy, S.; Jones, S.; Rosenthal, A.; Wen, G.; Schilhabel, M.; Gloeckner, G.; Nyakatura, G.; Siebert, R.; Schlegelberger, B.; Korenberg, J.; Chen, X.N.; Fujiyama, A.; Hattori, M.; Toyoda, A.; Yada, T.; Park, H.S.; Sakaki, Y.; Shimizu, N.; Asakawa, S.; Kawasaki, K.; Sasaki, T.; Shintani, A.; Shimizu, A.; Shibuya, K.; Kudoh, J.; Minoshima, S.; Ramser, J.; Seranski, P.; Hoff, C.; Poustka, A.; Reinhardt, R.; Lehrach, H.

    2001-01-01

    The human genome is by far the largest genome to be sequenced, and its size and complexity present many challenges for sequence assembly. The International Human Genome Sequencing Consortium constructed a map of the whole genome to enable the selection of clones for sequencing and for the accurate assembly of the genome sequence. Here we report the construction of the whole-genome bacterial artificial chromosome (BAC) map and its integration with previous landmark maps and information from mapping efforts focused on specific chromosomal regions. We also describe the integration of sequence data with the map.

  1. Enhancer Identification through Comparative Genomics

    Energy Technology Data Exchange (ETDEWEB)

    Visel, Axel; Bristow, James; Pennacchio, Len A.

    2006-10-01

    With the availability of genomic sequence from numerousvertebrates, a paradigm shift has occurred in the identification ofdistant-acting gene regulatory elements. In contrast to traditionalgene-centric studies in which investigators randomly scanned genomicfragments that flank genes of interest in functional assays, the modernapproach begins electronically with publicly available comparativesequence datasets that provide investigators with prioritized lists ofputative functional sequences based on their evolutionary conservation.However, although a large number of tools and resources are nowavailable, application of comparative genomic approaches remains far fromtrivial. In particular, it requires users to dynamically consider thespecies and methods for comparison depending on the specific biologicalquestion under investigation. While there is currently no single generalrule to this end, it is clear that when applied appropriately,comparative genomic approaches exponentially increase our power ingenerating biological hypotheses for subsequent experimentaltesting.

  2. Explosives, Genomics, and the Environment

    Directory of Open Access Journals (Sweden)

    Kieran C. O’Doherty

    2013-03-01

    Full Text Available RDX is an explosive that is also a neurotoxin and implicated in adverse health outcomes. Because of its widespread use in military and civilian operations, there is growing concern about potential environmental and health implications. One promising method of bioremediation involves genomic studies of soil microbes. These health concerns and technological issues intersect with social and political dimensions raising questions about public responses to genomic technologies and the degree of environmental accounting expected from the military. In cases of novel technologies entering into contested social spaces, public engagement can be useful to inform broader policy debates. Building on previous work, in this article, we outline the rationale, methods, and results of a public deliberation on these issues. To our knowledge, this is the first study of its kind on the issues of RDX pollution and microbial genomics, and thus provides an important baseline on public sentiment on these issues.

  3. The genome of Theobroma cacao.

    Science.gov (United States)

    Argout, Xavier; Salse, Jerome; Aury, Jean-Marc; Guiltinan, Mark J; Droc, Gaetan; Gouzy, Jerome; Allegre, Mathilde; Chaparro, Cristian; Legavre, Thierry; Maximova, Siela N; Abrouk, Michael; Murat, Florent; Fouet, Olivier; Poulain, Julie; Ruiz, Manuel; Roguet, Yolande; Rodier-Goud, Maguy; Barbosa-Neto, Jose Fernandes; Sabot, Francois; Kudrna, Dave; Ammiraju, Jetty Siva S; Schuster, Stephan C; Carlson, John E; Sallet, Erika; Schiex, Thomas; Dievart, Anne; Kramer, Melissa; Gelley, Laura; Shi, Zi; Bérard, Aurélie; Viot, Christopher; Boccara, Michel; Risterucci, Ange Marie; Guignon, Valentin; Sabau, Xavier; Axtell, Michael J; Ma, Zhaorong; Zhang, Yufan; Brown, Spencer; Bourge, Mickael; Golser, Wolfgang; Song, Xiang; Clement, Didier; Rivallan, Ronan; Tahi, Mathias; Akaza, Joseph Moroh; Pitollat, Bertrand; Gramacho, Karina; D'Hont, Angélique; Brunel, Dominique; Infante, Diogenes; Kebe, Ismael; Costet, Pierre; Wing, Rod; McCombie, W Richard; Guiderdoni, Emmanuel; Quetier, Francis; Panaud, Olivier; Wincker, Patrick; Bocs, Stephanie; Lanaud, Claire

    2011-02-01

    We sequenced and assembled the draft genome of Theobroma cacao, an economically important tropical-fruit tree crop that is the source of chocolate. This assembly corresponds to 76% of the estimated genome size and contains almost all previously described genes, with 82% of these genes anchored on the 10 T. cacao chromosomes. Analysis of this sequence information highlighted specific expansion of some gene families during evolution, for example, flavonoid-related genes. It also provides a major source of candidate genes for T. cacao improvement. Based on the inferred paleohistory of the T. cacao genome, we propose an evolutionary scenario whereby the ten T. cacao chromosomes were shaped from an ancestor through eleven chromosome fusions.

  4. Genomics, medicine and public health

    Directory of Open Access Journals (Sweden)

    Alexander M. Trbovich

    2006-12-01

    Full Text Available Public health genomics unifies the scientific disciplines of genetics and public health. Public health genomics aims to facilitate the transfer of newly acquired knowledge in genetic and molecular biology into classical medicine, to evaluate the currently available genetic tests, and to educate both the medical community and the general population about advancements in molecular and cell biology of medical interest. Due to various factors, the application of new genetic discoveries in classical medicine and the evaluation of the current genetic clinical tests occur at relatively slow paste. The challenge of public health genomics is to create the most effective modus for coexistence of new molecular and cell biology discoveries and classical medical techniques in applied medicine. The ultimate goal is to accomplish a truly individualized medical therapy.

  5. Genomic imprinting in farm animals.

    Science.gov (United States)

    Tian, Xiuchun Cindy

    2014-02-01

    The mouse is the first species in which genomic imprinting was studied. Imprinting research in farm species has lagged behind owing to a lack of sequencing and genetic background information, as well as long generation intervals and high costs in tissue collection. Since the creation of Dolly, the first cloned mammal from an adult sheep, studies on genomic imprinting in domestic species have accelerated because animals from cloning and other assisted reproductive technologies exhibit phenotypes of imprinting disruptions. Although this review focuses on new developments in farm animals, most of the imprinting mechanism information was derived from the mouse.

  6. Genomic Signals of Reoriented ORFs

    Directory of Open Access Journals (Sweden)

    Paul Dan Cristea

    2004-01-01

    Full Text Available Complex representation of nucleotides is used to convert DNA sequences into complex digital genomic signals. The analysis of the cumulated phase and unwrapped phase of DNA genomic signals reveals large-scale features of eukaryote and prokaryote chromosomes that result from statistical regularities of base and base-pair distributions along DNA strands. By reorienting the chromosome coding regions, a “hidden” linear variation of the cumulated phase has been revealed, along with the conspicuous almost linear variation of the unwrapped phase. A model of chromosome longitudinal structure is inferred on these bases.

  7. Easyfig: a genome comparison visualizer.

    Science.gov (United States)

    Sullivan, Mitchell J; Petty, Nicola K; Beatson, Scott A

    2011-04-01

    Easyfig is a Python application for creating linear comparison figures of multiple genomic loci with an easy-to-use graphical user interface. BLAST comparisons between multiple genomic regions, ranging from single genes to whole prokaryote chromosomes, can be generated, visualized and interactively coloured, enabling a rapid transition between analysis and the preparation of publication quality figures. Easyfig is freely available (under a GPL license) for download (for Mac OS X, Unix and Microsoft Windows) from the SourceForge web site: http://easyfig.sourceforge.net/.

  8. Fungal genomics beyond Saccharomyces cerevisiae?

    DEFF Research Database (Denmark)

    Hofmann, Gerald; Mcintyre, Mhairi; Nielsen, Jens

    2003-01-01

    Fungi are used extensively in both fundamental research and industrial applications. Saccharomyces cerevisiae has been the model organism for fungal research for many years, particularly in functional genomics. However, considering the diversity within the fungal kingdom, it is obvious...... that the application of the existing methods of genome, transcriptome, proteome and metabolome analysis to other fungi has enormous potential, especially for the production of food and food ingredients. The developments in the past year demonstrate that we have only just started to exploit this potential....

  9. Genome editing comes of age.

    Science.gov (United States)

    Kim, Jin-Soo

    2016-09-01

    Genome editing harnesses programmable nucleases to cut and paste genetic information in a targeted manner in living cells and organisms. Here, I review the development of programmable nucleases, including zinc finger nucleases (ZFNs), TAL (transcription-activator-like) effector nucleases (TALENs) and CRISPR (cluster of regularly interspaced palindromic repeats)-Cas9 (CRISPR-associated protein 9) RNA-guided endonucleases (RGENs). I specifically highlight the key advances that set the foundation for the rapid and widespread implementation of CRISPR-Cas9 genome editing approaches that has revolutionized the field.

  10. Genomic composition factors affect codon usage in porcine genome ...

    African Journals Online (AJOL)

    The objective of the study was to determine the codon usage bias in the porcine genome and decipher its determinants. To investigate the underlying mechanisms of codon bias, the coding sequence (CDS) from the swine reference sequence (ssc10.2) was extracted using Biomart. An in house built Perl script was used to ...

  11. [Nutritional genomics: an approach to the genome-environment interaction].

    Science.gov (United States)

    Xacur-García, Fiona; Castillo-Quan, Jorge I; Hernández-Escalante, Víctor M; Laviada-Molina, Hugo

    2008-11-01

    Nutritional genomics forms part of the genomic sciences and addresses the interaction between genes and the human diet, its influence on metabolism and subsequent susceptibility to develop common diseases. It encompasses both nutrigenomics, which explores the effects of nutrients on the genome, proteome and metabolome; and nutrigenetics, that explores the effects of genetic variations on the diet/disease interaction. A number of mechanisms drive the gene/diet interaction: elements in the diet can act as links for transcription factor receptors and after intermediary concentrations, thereby modifying chromatin and impacting genetic regulation; affect signal pathways, regulating phosphorylation of tyrosine in receptors; decrease signaling through the inositol pathway; and act through epigenetic mechanisms, silencing DNA fragments by methylation of cytosine. The signals generated by polyunsaturated fatty acids are so powerful that they can even bypass insulin mediated lipogenesis, stimulated by carbohydrates. Some fatty acids modify the expression of genes that participate in fatty acid transport by lipoproteins. Nutritional genomics has myriad possible therapeutic and preventive applications: in patients with enzymatic deficiencies; in those with a genetic predisposition to complex diseases such as dyslipidemia, diabetes and cancer; in those that already suffer these diseases; in those with altered mood or memory; during the aging process; in pregnant women; and as a preventive measure in the healthy population.

  12. Genomic composition factors affect codon usage in porcine genome

    African Journals Online (AJOL)

    j.khobondo

    2015-01-28

    Jan 28, 2015 ... expression of target genes in vivo or in vitro and improve the accuracy of gene prediction from genomic sequences thus maximizing ... These biological breakthroughs revealed the importance of studying the degeneracy of ... diversity, gene expression and evolution, and adaptation to micro environment.

  13. Enhancing the genome editing toolbox: genome wide CRISPR arrayed libraries.

    Science.gov (United States)

    Metzakopian, Emmanouil; Strong, Alex; Iyer, Vivek; Hodgkins, Alex; Tzelepis, Konstantinos; Antunes, Liliana; Friedrich, Mathias J; Kang, Qiaohua; Davidson, Teresa; Lamberth, Jacob; Hoffmann, Christina; Davis, Gregory D; Vassiliou, George S; Skarnes, William C; Bradley, Allan

    2017-05-22

    CRISPR-Cas9 technology has accelerated biological research becoming routine for many laboratories. It is rapidly replacing conventional gene editing techniques and has high utility for both genome-wide and gene-focussed applications. Here we present the first individually cloned CRISPR-Cas9 genome wide arrayed sgRNA libraries covering 17,166 human and 20,430 mouse genes at a complexity of 34,332 sgRNAs for human and 40,860 sgRNAs for the mouse genome. For flexibility in generating stable cell lines the sgRNAs have been cloned in a lentivirus backbone containing PiggyBac transposase recognition elements together with fluorescent and drug selection markers. Over 95% of tested sgRNA induced specific DNA cleavage as measured by CEL-1 assays. Furthermore, sgRNA targeting GPI anchor protein pathway genes induced loss of function mutations in human and mouse cell lines measured by FLAER labelling. These arrayed libraries offer the prospect for performing screens on individual genes, combinations as well as larger gene sets. They also facilitate rapid deconvolution of signals from genome-wide screens. This set of vectors provide an organized comprehensive gene editing toolbox of considerable scientific value.

  14. The Phaeodactylum genome reveals the evolutionary history of diatom genomes

    Czech Academy of Sciences Publication Activity Database

    Bowler, Ch.; Allen, A. E.; Badger, J. H.; Grimwood, J.; Jabbari, K.; Kuo, A.; Maheswari, U.; Martens, C.; Maumus, F.; Otillar, R. P.; Rayko, E.; Salamov, A.; Vandepoele, K.; Beszteri, B.; Gruber, A.; Heijde, M.; Katinka, M.; Mock, T.; Valentin, K.; Verret, F.; Berges, J. A.; Brownlee, C.; Cadoret, J.-P.; Chiovitti, A.; Choi, Ch. J.; Coesel, S.; De Martino, A.; Detter, J. Ch.; Durkin, C.; Falciatore, A.; Fournet, J.; Haruta, M.; Huysman, M. J. J.; Jenkins, B. D.; Jiroutová, Kateřina; Jorgensen, R. E.; Joubert, Y.; Kaplan, A.; Kröger, N.; Kroth, P. G.; La Roche, J.; Lindquist, E.; Lommer, M.; Martin–Jézéquel, V.; Lopez, P. J.; Lucas, S.; Mangogna, M.; McGinnis, K.; Medlin, L. K.; Montsant, A.; Oudot–Le Secq, M.-P.; Napoli, C.; Oborník, Miroslav; Schnitzler Parker, M.; Petit, J.-L.; Porcel, B. M.; Poulsen, N.; Robison, M.; Rychlewski, L.; Rynearson, T. A.; Schmutz, J.; Shapiro, H.; Siaut, M.; Stanley, M.; Sussman, M. R.; Taylor, A. R.; Vardi, A.; von Dassow, P.; Vyverman, W.; Willis, A.; Wyrwicz, L. S.; Rokhsar, D. S.; Weissenbach, J.; Armbrust, E. V.; Green, B. R.; Van de Peer, Y.; Grigoriev, I. V.

    2008-01-01

    Roč. 456, 13-11-2008 (2008), s. 239-244 ISSN 0028-0836 Institutional research plan: CEZ:AV0Z60220518 Keywords : Phaeodactylum * genome * evolution * diatom Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 31.434, year: 2008

  15. Genome surfing as driver of microbial genomic diversity

    Science.gov (United States)

    Historical changes in population size, such as those caused by demographic range expansions, can produce nonadaptive changes in genomic diversity through mechanisms such as gene surfing. We propose that demographic range expansion of a microbial population capable of horizontal gene exchange can res...

  16. An Exploration into Fern Genome Space.

    Science.gov (United States)

    Wolf, Paul G; Sessa, Emily B; Marchant, Daniel Blaine; Li, Fay-Wei; Rothfels, Carl J; Sigel, Erin M; Gitzendanner, Matthew A; Visger, Clayton J; Banks, Jo Ann; Soltis, Douglas E; Soltis, Pamela S; Pryer, Kathleen M; Der, Joshua P

    2015-08-26

    Ferns are one of the few remaining major clades of land plants for which a complete genome sequence is lacking. Knowledge of genome space in ferns will enable broad-scale comparative analyses of land plant genes and genomes, provide insights into genome evolution across green plants, and shed light on genetic and genomic features that characterize ferns, such as their high chromosome numbers and large genome sizes. As part of an initial exploration into fern genome space, we used a whole genome shotgun sequencing approach to obtain low-density coverage (∼0.4X to 2X) for six fern species from the Polypodiales (Ceratopteris, Pteridium, Polypodium, Cystopteris), Cyatheales (Plagiogyria), and Gleicheniales (Dipteris). We explore these data to characterize the proportion of the nuclear genome represented by repetitive sequences (including DNA transposons, retrotransposons, ribosomal DNA, and simple repeats) and protein-coding genes, and to extract chloroplast and mitochondrial genome sequences. Such initial sweeps of fern genomes can provide information useful for selecting a promising candidate fern species for whole genome sequencing. We also describe variation of genomic traits across our sample and highlight some differences and similarities in repeat structure between ferns and seed plants. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  17. Genome Size Dynamics and Evolution in Monocots

    Directory of Open Access Journals (Sweden)

    Ilia J. Leitch

    2010-01-01

    Full Text Available Monocot genomic diversity includes striking variation at many levels. This paper compares various genomic characters (e.g., range of chromosome numbers and ploidy levels, occurrence of endopolyploidy, GC content, chromosome packaging and organization, genome size between monocots and the remaining angiosperms to discern just how distinctive monocot genomes are. One of the most notable features of monocots is their wide range and diversity of genome sizes, including the species with the largest genome so far reported in plants. This genomic character is analysed in greater detail, within a phylogenetic context. By surveying available genome size and chromosome data it is apparent that different monocot orders follow distinctive modes of genome size and chromosome evolution. Further insights into genome size-evolution and dynamics were obtained using statistical modelling approaches to reconstruct the ancestral genome size at key nodes across the monocot phylogenetic tree. Such approaches reveal that while the ancestral genome size of all monocots was small (1C=1.9 pg, there have been several major increases and decreases during monocot evolution. In addition, notable increases in the rates of genome size-evolution were found in Asparagales and Poales compared with other monocot lineages.

  18. Challenges to genome sequence dissection in sweetpotato

    Science.gov (United States)

    Isobe, Sachiko; Shirasawa, Kenta; Hirakawa, Hideki

    2017-01-01

    The development of next generation sequencing (NGS) technologies has enabled the determination of whole genome sequences in many non-model plant species. However, genome sequencing in sweetpotato (Ipomoea batatas (L.) Lam) is still difficult because of the hexaploid genome structure. Previous studies suggested that a diploid wild relative, I. trifida (H.B.K.) Don., is the most possible ancestor of sweetpotato. Therefore, the genetic and genomic features of I. trifida have been studied as a potential reference for sweetpotato. Meanwhile, several research groups have begun the challenging task of directly sequencing the sweetpotato genome. In this manuscript, we review the recent results and activities of large-scale genome and transcriptome analysis related to genome sequence dissection in sweetpotato under the sections as follows: I. trifida genome and transcript sequencing, genome sequences of I. nil (Japanese morning glory), transcript sequences in sweetpotato, chloroplast sequences, transposable elements and transfer DNA. The recent international activities of de novo whole genome sequencing in sweetpotato are also described. The large-scale publically available genome and transcript sequence resources and the international genome sequencing streams are expected to promote the genome sequence dissection in sweetpotato. PMID:28465666

  19. Burkholderia pseudomallei genome plasticity associated with genomic island variation

    Directory of Open Access Journals (Sweden)

    Currie Bart J

    2008-04-01

    Full Text Available Abstract Background Burkholderia pseudomallei is a soil-dwelling saprophyte and the cause of melioidosis. Horizontal gene transfer contributes to the genetic diversity of this pathogen and may be an important determinant of virulence potential. The genome contains genomic island (GI regions that encode a broad array of functions. Although there is some evidence for the variable distribution of genomic islands in B. pseudomallei isolates, little is known about the extent of variation between related strains or their association with disease or environmental survival. Results Five islands from B. pseudomallei strain K96243 were chosen as representatives of different types of genomic islands present in this strain, and their presence investigated in other B. pseudomallei. In silico analysis of 10 B. pseudomallei genome sequences provided evidence for the variable presence of these regions, together with micro-evolutionary changes that generate GI diversity. The diversity of GIs in 186 isolates from NE Thailand (83 environmental and 103 clinical isolates was investigated using multiplex PCR screening. The proportion of all isolates positive by PCR ranged from 12% for a prophage-like island (GI 9, to 76% for a metabolic island (GI 16. The presence of each of the five GIs did not differ between environmental and disease-associated isolates (p > 0.05 for all five islands. The cumulative number of GIs per isolate for the 186 isolates ranged from 0 to 5 (median 2, IQR 1 to 3. The distribution of cumulative GI number did not differ between environmental and disease-associated isolates (p = 0.27. The presence of GIs was defined for the three largest clones in this collection (each defined as a single sequence type, ST, by multilocus sequence typing; these were ST 70 (n = 15 isolates, ST 54 (n = 11, and ST 167 (n = 9. The rapid loss and/or acquisition of gene islands was observed within individual clones. Comparisons were drawn between isolates obtained

  20. Advancing Eucalyptus Genomics: Cytogenomics Reveals Conservation of Eucalyptus Genomes

    Science.gov (United States)

    Ribeiro, Teresa; Barrela, Ricardo M.; Bergès, Hélène; Marques, Cristina; Loureiro, João; Morais-Cecílio, Leonor; Paiva, Jorge A. P.

    2016-01-01

    The genus Eucalyptus encloses several species with high ecological and economic value, being the subgenus Symphyomyrtus one of the most important. Species such as E. grandis and E. globulus are well characterized at the molecular level but knowledge regarding genome and chromosome organization is very scarce. Here we characterized and compared the karyotypes of three economically important species, E. grandis, E. globulus, and E. calmadulensis, and three with ecological relevance, E. pulverulenta, E. cornuta, and E. occidentalis, through an integrative approach including genome size estimation, fluorochrome banding, rDNA FISH, and BAC landing comprising genes involved in lignin biosynthesis. All karyotypes show a high degree of conservation with pericentromeric 35S and 5S rDNA loci in the first and third pairs, respectively. GC-rich heterochromatin was restricted to the 35S rDNA locus while the AT-rich heterochromatin pattern was species-specific. The slight differences in karyotype formulas and distribution of AT-rich heterochromatin, along with genome sizes estimations, support the idea of Eucalyptus genome evolution by local expansions of heterochromatin clusters. The unusual co-localization of both rDNA with AT-rich heterochromatin was attributed mainly to the presence of silent transposable elements in those loci. The cinnamoyl CoA reductase gene (CCR1) previously assessed to linkage group 10 (LG10) was clearly localized distally at the long arm of chromosome 9 establishing an unexpected correlation between the cytogenetic chromosome 9 and the LG10. Our work is novel and contributes to the understanding of Eucalyptus genome organization which is essential to develop successful advanced breeding strategies for this genus. PMID:27148332

  1. Implementing genomics and pharmacogenomics in the clinic: The National Human Genome Research Institute’s genomic medicine portfolio

    Science.gov (United States)

    Manolio, Teri A.

    2016-01-01

    Increasing knowledge about the influence of genetic variation on human health and growing availability of reliable, cost-effective genetic testing have spurred the implementation of genomic medicine in the clinic. As defined by the National Human Genome Research Institute (NHGRI), genomic medicine uses an individual’s genetic information in his or her clinical care, and has begun to be applied effectively in areas such as cancer genomics, pharmacogenomics, and rare and undiagnosed diseases. In 2011 NHGRI published its strategic vision for the future of genomic research, including an ambitious research agenda to facilitate and promote the implementation of genomic medicine. To realize this agenda, NHGRI is consulting and facilitating collaborations with the external research community through a series of “Genomic Medicine Meetings,” under the guidance and leadership of the National Advisory Council on Human Genome Research. These meetings have identified and begun to address significant obstacles to implementation, such as lack of evidence of efficacy, limited availability of genomics expertise and testing, lack of standards, and diffficulties in integrating genomic results into electronic medical records. The six research and dissemination initiatives comprising NHGRI’s genomic research portfolio are designed to speed the evaluation and incorporation, where appropriate, of genomic technologies and findings into routine clinical care. Actual adoption of successful approaches in clinical care will depend upon the willingness, interest, and energy of professional societies, practitioners, patients, and payers to promote their responsible use and share their experiences in doing so. PMID:27612677

  2. Genome size variation in the genus Avena.

    Science.gov (United States)

    Yan, Honghai; Martin, Sara L; Bekele, Wubishet A; Latta, Robert G; Diederichsen, Axel; Peng, Yuanying; Tinker, Nicholas A

    2016-03-01

    Genome size is an indicator of evolutionary distance and a metric for genome characterization. Here, we report accurate estimates of genome size in 99 accessions from 26 species of Avena. We demonstrate that the average genome size of C genome diploid species (2C = 10.26 pg) is 15% larger than that of A genome species (2C = 8.95 pg), and that this difference likely accounts for a progression of size among tetraploid species, where AB Avena have experienced genome downsizing in relation to their diploid progenitors. Genome size measurements could provide additional quality control for species identification in germplasm collections, especially in cases where diploid and polyploid species have similar morphology.

  3. Strategies and tools for whole genome alignments

    Energy Technology Data Exchange (ETDEWEB)

    Couronne, Olivier; Poliakov, Alexander; Bray, Nicolas; Ishkhanov,Tigran; Ryaboy, Dmitriy; Rubin, Edward; Pachter, Lior; Dubchak, Inna

    2002-11-25

    The availability of the assembled mouse genome makespossible, for the first time, an alignment and comparison of two largevertebrate genomes. We have investigated different strategies ofalignment for the subsequent analysis of conservation of genomes that areeffective for different quality assemblies. These strategies were appliedto the comparison of the working draft of the human genome with the MouseGenome Sequencing Consortium assembly, as well as other intermediatemouse assemblies. Our methods are fast and the resulting alignmentsexhibit a high degree of sensitivity, covering more than 90 percent ofknown coding exons in the human genome. We have obtained such coveragewhile preserving specificity. With a view towards the end user, we havedeveloped a suite of tools and websites for automatically aligning, andsubsequently browsing and working with whole genome comparisons. Wedescribe the use of these tools to identify conserved non-coding regionsbetween the human and mouse genomes, some of which have not beenidentified by other methods.

  4. V-GAP: Viral genome assembly pipeline

    KAUST Repository

    Nakamura, Yoji

    2015-10-22

    Next-generation sequencing technologies have allowed the rapid determination of the complete genomes of many organisms. Although shotgun sequences from large genome organisms are still difficult to reconstruct perfect contigs each of which represents a full chromosome, those from small genomes have been assembled successfully into a very small number of contigs. In this study, we show that shotgun reads from phage genomes can be reconstructed into a single contig by controlling the number of read sequences used in de novo assembly. We have developed a pipeline to assemble small viral genomes with good reliability using a resampling method from shotgun data. This pipeline, named V-GAP (Viral Genome Assembly Pipeline), will contribute to the rapid genome typing of viruses, which are highly divergent, and thus will meet the increasing need for viral genome comparisons in metagenomic studies.

  5. Gramene database: navigating plant comparative genomics resources

    Science.gov (United States)

    Gramene (http://www.gramene.org) is an online, open source, curated resource for plant comparative genomics and pathway analysis designed to support researchers working in plant genomics, breeding, evolutionary biology, system biology, and metabolic engineering. It exploits phylogenetic relationship...

  6. India, Genomic diversity & Disease susceptibility

    Indian Academy of Sciences (India)

    Table of contents. India, Genomic diversity & Disease susceptibility · India, a paradise for Genetic Studies · Involved in earlier stages of Immune response protecting us from Diseases, Responsible for kidney and other transplant rejections Inherited from our parents · PowerPoint Presentation · Slide 5 · Slide 6 · Slide 7.

  7. The genome of a songbird

    Science.gov (United States)

    Warren, Wesley C.; Clayton, David F.; Ellegren, Hans; Arnold, Arthur P.; Hillier, LaDeana W.; Künstner, Axel; Searle, Steve; White, Simon; Vilella, Albert J.; Fairley, Susan; Heger, Andreas; Kong, Lesheng; Ponting, Chris P.; Jarvis, Erich D.; Mello, Claudio V.; Minx, Pat; Lovell, Peter; Velho, Tarciso A. F.; Ferris, Margaret; Balakrishnan, Christopher N.; Sinha, Saurabh; Blatti, Charles; London, Sarah E.; Li, Yun; Lin, Ya-Chi; George, Julia; Sweedler, Jonathan; Southey, Bruce; Gunaratne, Preethi; Watson, Michael; Nam, Kiwoong; Backström, Niclas; Smeds, Linnea; Nabholz, Benoit; Itoh, Yuichiro; Whitney, Osceola; Pfenning, Andreas R.; Howard, Jason; Völker, Martin; Skinner, Bejamin M.; Griffin, Darren K.; Ye, Liang; McLaren, William M.; Flicek, Paul; Quesada, Victor; Velasco, Gloria; Lopez-Otin, Carlos; Puente, Xose S.; Olender, Tsviya; Lancet, Doron; Smit, Arian F. A.; Hubley, Robert; Konkel, Miriam K.; Walker, Jerilyn A.; Batzer, Mark A.; Gu, Wanjun; Pollock, David D.; Chen, Lin; Cheng, Ze; Eichler, Evan E.; Stapley, Jessica; Slate, Jon; Ekblom, Robert; Birkhead, Tim; Burke, Terry; Burt, David; Scharff, Constance; Adam, Iris; Richard, Hugues; Sultan, Marc; Soldatov, Alexey; Lehrach, Hans; Edwards, Scott V.; Yang, Shiaw-Pyng; Li, XiaoChing; Graves, Tina; Fulton, Lucinda; Nelson, Joanne; Chinwalla, Asif; Hou, Shunfeng; Mardis, Elaine R.; Wilson, Richard K.

    2010-01-01

    The zebra finch is an important model organism in several fields1,2 with unique relevance to human neuroscience3,4. Like other songbirds, the zebra finch communicates through learned vocalizations, an ability otherwise documented only in humans and a few other animals and lacking in the chicken5—the only bird with a sequenced genome until now6. Here we present a structural, functional and comparative analysis of the genome sequence of the zebra finch (Taeniopygia guttata), which is a songbird belonging to the large avian order Passeriformes7. We find that the overall structures of the genomes are similar in zebra finch and chicken, but they differ in many intrachromosomal rearrangements, lineage-specific gene family expansions, the number of long-terminal-repeat-based retrotransposons, and mechanisms of sex chromosome dosage compensation. We show that song behaviour engages gene regulatory networks in the zebra finch brain, altering the expression of long non-coding RNAs, microRNAs, transcription factors and their targets. We also show evidence for rapid molecular evolution in the songbird lineage of genes that are regulated during song experience. These results indicate an active involvement of the genome in neural processes underlying vocal communication and identify potential genetic substrates for the evolution and regulation of this behaviour. PMID:20360741

  8. Genome position and gene amplification

    Czech Academy of Sciences Publication Activity Database

    Jirsová, Pavla; Snijders, A.M.; Kwek, S.; Roydasgupta, R.; Fridlyand, J.; Tokuyasu, T.; Pinkel, D.; Albertson, D. G.

    2007-01-01

    Roč. 8, č. 6 (2007), r120 ISSN 1474-760X Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : gene amplification * array comparative genomic hybridization * oncogene Subject RIV: BO - Biophysics Impact factor: 6.589, year: 2007

  9. Fungal genome resources at NCBI

    Science.gov (United States)

    Robbertse, B.; Tatusova, T.

    2011-01-01

    The National Center for Biotechnology Information (NCBI) is well known for the nucleotide sequence archive, GenBank and sequence analysis tool BLAST. However, NCBI integrates many types of biomolecular data from variety of sources and makes it available to the scientific community as interactive web resources as well as organized releases of bulk data. These tools are available to explore and compare fungal genomes. Searching all databases with Fungi [organism] at http://www.ncbi.nlm.nih.gov/ is the quickest way to find resources of interest with fungal entries. Some tools though are resources specific and can be indirectly accessed from a particular database in the Entrez system. These include graphical viewers and comparative analysis tools such as TaxPlot, TaxMap and UniGene DDD (found via UniGene Homepage). Gene and BioProject pages also serve as portals to external data such as community annotation websites, BioGrid and UniProt. There are many different ways of accessing genomic data at NCBI. Depending on the focus and goal of research projects or the level of interest, a user would select a particular route for accessing genomic databases and resources. This review article describes methods of accessing fungal genome data and provides examples that illustrate the use of analysis tools. PMID:22737589

  10. Scalable Computing for Evolutionary Genomics

    NARCIS (Netherlands)

    Prins, J.C.P.; Belhachemi, D.; Möller, S.; Smant, G.

    2012-01-01

    Genomic data analysis in evolutionary biology is becoming so computationally intensive that analysis of multiple hypotheses and scenarios takes too long on a single desktop computer. In this chapter, we discuss techniques for scaling computations through parallelization of calculations, after giving

  11. Ecological Genomics of Marine Picocyanobacteria†

    Science.gov (United States)

    Scanlan, D. J.; Ostrowski, M.; Mazard, S.; Dufresne, A.; Garczarek, L.; Hess, W. R.; Post, A. F.; Hagemann, M.; Paulsen, I.; Partensky, F.

    2009-01-01

    Summary: Marine picocyanobacteria of the genera Prochlorococcus and Synechococcus numerically dominate the picophytoplankton of the world ocean, making a key contribution to global primary production. Prochlorococcus was isolated around 20 years ago and is probably the most abundant photosynthetic organism on Earth. The genus comprises specific ecotypes which are phylogenetically distinct and differ markedly in their photophysiology, allowing growth over a broad range of light and nutrient conditions within the 45°N to 40°S latitudinal belt that they occupy. Synechococcus and Prochlorococcus are closely related, together forming a discrete picophytoplankton clade, but are distinguishable by their possession of dissimilar light-harvesting apparatuses and differences in cell size and elemental composition. Synechococcus strains have a ubiquitous oceanic distribution compared to that of Prochlorococcus strains and are characterized by phylogenetically discrete lineages with a wide range of pigmentation. In this review, we put our current knowledge of marine picocyanobacterial genomics into an environmental context and present previously unpublished genomic information arising from extensive genomic comparisons in order to provide insights into the adaptations of these marine microbes to their environment and how they are reflected at the genomic level. PMID:19487728

  12. Biclustering Sparse Binary Genomic Data

    NARCIS (Netherlands)

    Van Uitert, M.; Meuleman, W.; Wessels, L.F.A.

    2008-01-01

    Genomic datasets often consist of large, binary, sparse data matrices. In such a dataset, one is often interested in finding contiguous blocks that (mostly) contain ones. This is a biclustering problem, and while many algorithms have been proposed to deal with gene expression data, only two

  13. Genomic Heritability: What Is It?

    DEFF Research Database (Denmark)

    de los Campos, Gustavo; Sorensen, Daniel; Gianola, Daniel

    2015-01-01

    Whole-genome regression methods are being increasingly used for the analysis and prediction of complex traits and diseases. In human genetics, these methods are commonly used for inferences about genetic parameters, such as the amount of genetic variance among individuals or the proportion of phe...

  14. Bioinformatica ten behoeve van genomics

    NARCIS (Netherlands)

    Pennings JLA; Hoebee B; TOX

    2007-01-01

    Sinds enkele jaren wordt op het RIVM genomicsonderzoek uitgevoerd. Genomics omvat grootschalig onderzoek naar het erfelijk materiaal (DNA) van organismen. Dit onderzoek levert inzicht op in de manier waarop erfelijke eigenschappen zich vertalen naar het functioneren van een cel, en uiteindelijk

  15. Nutritional genomics and personalized diet

    African Journals Online (AJOL)

    Nagwa E.A. Gaboon

    Nutritional genomics. Abstract Nutritional genetics is considered as the combination of nutrigenomics and nutrigenetics. Nutrigenomics is establishing the .... on the knowledge of nutritional requirements, nutritional status, and genotype (i.e., person- alized nutrition) can be used to prevent, mitigate, or cure chronic disease. 3.

  16. The genome of Chenopodium quinoa

    NARCIS (Netherlands)

    Jarvis, D.E.; Shwen Ho, Yung; Lightfoot, Damien J.; Schmöckel, Sandra M.; Li, Bo; Borm, T.J.A.; Ohyanagi, Hajime; Mineta, Katsuhiko; Mitchell, Craig T.; Saber, Noha; Kharbatia, Najeh M.; Rupper, Ryan R.; Sharp, Aaron R.; Dally, Nadine; Boughton, Berin A.; Woo, Yong H.; Gao, Ge; Schijlen, E.G.W.M.; Guo, Xiujie; Momin, Afaque A.; Negräo, Sónia; Al-Babili, Salim; Gehring, Christoph; Roessner, Ute; Jung, Christian; Murphy, Kevin; Arold, Stefan T.; Gojobori, Takashi; Linden, van der C.G.; Loo, van E.N.; Jellen, Eric N.; Maughan, Peter J.; Tester, Mark

    2017-01-01

    Chenopodium quinoa (quinoa) is a highly nutritious grain identified as an important crop to improve world food security. Unfortunately, few resources are available to facilitate its genetic improvement. Here we report the assembly of a high-quality, chromosome-scale reference genome sequence for

  17. Searching and Indexing Genomic Databases via Kernelization

    Directory of Open Access Journals (Sweden)

    Travis eGagie

    2015-02-01

    Full Text Available The rapid advance of DNA sequencing technologies has yielded databases of thousands of genomes. To search and index these databases effectively, it is important that we take advantage of the similarity between those genomes. Several authors have recently suggested searching or indexing only one reference genome and the parts of the other genomes where they differ. In this paper we survey the twenty-year history of this idea and discuss its relation to kernelization in parameterized complexity.

  18. Searching and Indexing Genomic Databases via Kernelization.

    Science.gov (United States)

    Gagie, Travis; Puglisi, Simon J

    2015-01-01

    The rapid advance of DNA sequencing technologies has yielded databases of thousands of genomes. To search and index these databases effectively, it is important that we take advantage of the similarity between those genomes. Several authors have recently suggested searching or indexing only one reference genome and the parts of the other genomes where they differ. In this paper, we survey the 20-year history of this idea and discuss its relation to kernelization in parameterized complexity.

  19. Genomics-assisted breeding in fruit trees

    OpenAIRE

    Iwata, Hiroyoshi; Minamikawa, Mai F.; Kajiya-Kanegae, Hiromi; Ishimori, Motoyuki; Hayashi, Takeshi

    2016-01-01

    Recent advancements in genomic analysis technologies have opened up new avenues to promote the efficiency of plant breeding. Novel genomics-based approaches for plant breeding and genetics research, such as genome-wide association studies (GWAS) and genomic selection (GS), are useful, especially in fruit tree breeding. The breeding of fruit trees is hindered by their long generation time, large plant size, long juvenile phase, and the necessity to wait for the physiological maturity of the pl...

  20. Meristem micropropagation of cassava (Manihot esculenta) evokes genome-wide changes in DNA methylation.

    Science.gov (United States)

    Kitimu, Shedrack R; Taylor, Julian; March, Timothy J; Tairo, Fred; Wilkinson, Mike J; Rodríguez López, Carlos M

    2015-01-01

    There is great interest in the phenotypic, genetic and epigenetic changes associated with plant in vitro culture known as somaclonal variation. In vitro propagation systems that are based on the use of microcuttings or meristem cultures are considered analogous to clonal cuttings and so widely viewed to be largely free from such somaclonal effects. In this study, we surveyed for epigenetic changes during propagation by meristem culture and by field cuttings in five cassava (Manihot esculenta) cultivars. Principal Co-ordinate Analysis of profiles generated by methylation-sensitive amplified polymorphism revealed clear divergence between samples taken from field-grown cuttings and those recovered from meristem culture. There was also good separation between the tissues of field samples but this effect was less distinct among the meristem culture materials. Application of methylation-sensitive Genotype by sequencing identified 105 candidate epimarks that distinguish between field cutting and meristem culture samples. Cross referencing the sequences of these epimarks to the draft cassava genome revealed 102 sites associated with genes whose homologs have been implicated in a range of fundamental biological processes including cell differentiation, development, sugar metabolism, DNA methylation, stress response, photosynthesis, and transposon activation. We explore the relevance of these findings for the selection of micropropagation systems for use on this and other crops.

  1. GRAbB : Selective Assembly of Genomic Regions, a New Niche for Genomic Research

    NARCIS (Netherlands)

    Brankovics, Balázs; Zhang, Hao; van Diepeningen, Anne D; van der Lee, Theo A J; Waalwijk, Cees; de Hoog, G Sybren

    GRAbB (Genomic Region Assembly by Baiting) is a new program that is dedicated to assemble specific genomic regions from NGS data. This approach is especially useful when dealing with multi copy regions, such as mitochondrial genome and the rDNA repeat region, parts of the genome that are often

  2. Genomic Organization of Leishmania Species

    Directory of Open Access Journals (Sweden)

    B Kazemi

    2011-09-01

    Full Text Available Leishmania is a protozoan parasite belonging to the family Trypanosomatidae, which is found among 88 different countries. The parasite lives as an amastigote in vertebrate macro­phages and as a promastigote in the digestive tract of sand fly. It can be cultured in the laboratory us­ing appropriate culture media. Although the sexual cycle of Leishmania has not been observed during the promastigote and amastigote stages, it has been reported by some researchers. Leishma­nia has eukaryotic cell organization. Cell culture is convenient and cost effective, and because posttranslational modifications are common processes in the cultured cells, the cells are used as hosts for preparing eukaryotic recombinant proteins for research. Several transcripts of rDNA in the Leishmania genome are suitable regions for conducting gene transfer. Old World Leishmania spp. has 36 chromosomes, while New World Leishmania spp. has 34 or 35 chromo­somes. The genomic organization and parasitic characteristics have been investigated. Leishmania spp. has a unique genomic organization among eukaryotes; the genes do not have introns, and the chromosomes are smaller with larger numbers of genes confined to a smaller space within the nucleus. Leishmania spp. genes are organized on one or both DNA strands and are transcribed as polycistronic (prokaryotic-like transcripts from undefined promoters. Regulation of gene expres­sion in the members of Trypanosomatidae differs from that in other eukaryotes. The trans-splic­ing phenomenon is a necessary step for mRNA processing in lower eukaryotes and is observed in Leishmania spp. Another particular feature of RNA editing in Leishmania spp. is that mitochon­drial genes encoding respiratory enzymes are edited and transcribed. This review will discuss the chromosomal and mitochondrial (kinetoplast genomes of Leishmania spp. as well as the phenome­non of RNA editing in the kinetoplast genome.

  3. International network of cancer genome projects

    NARCIS (Netherlands)

    Hudson, Thomas J.; Anderson, Warwick; Aretz, Axel; Barker, Anna D.; Bell, Cindy; Bernabé, Rosa R.; Bhan, M. K.; Calvo, Fabien; Eerola, Iiro; Gerhard, Daniela S.; Guttmacher, Alan; Guyer, Mark; Hemsley, Fiona M.; Jennings, Jennifer L.; Kerr, David; Klatt, Peter; Kolar, Patrik; Kusuda, Jun; Lane, David P.; Laplace, Frank; Lu, Youyong; Nettekoven, Gerd; Ozenberger, Brad; Peterson, Jane; Rao, T. S.; Remacle, Jacques; Schafer, Alan J.; Shibata, Tatsuhiro; Stratton, Michael R.; Vockley, Joseph G.; Watanabe, Koichi; Yang, Huanming; Yuen, Matthew M. F.; Knoppers, Bartha M.; Bobrow, Martin; Cambon-Thomsen, Anne; Dressler, Lynn G.; Dyke, Stephanie O. M.; Joly, Yann; Kato, Kazuto; Kennedy, Karen L.; Nicolás, Pilar; Parker, Michael J.; Rial-Sebbag, Emmanuelle; Romeo-Casabona, Carlos M.; Shaw, Kenna M.; Wallace, Susan; Wiesner, Georgia L.; Zeps, Nikolajs; Lichter, Peter; Biankin, Andrew V.; Chabannon, Christian; Chin, Lynda; Clément, Bruno; de Alava, Enrique; Degos, Françoise; Ferguson, Martin L.; Geary, Peter; Hayes, D. Neil; Johns, Amber L.; Kasprzyk, Arek; Nakagawa, Hidewaki; Penny, Robert; Piris, Miguel A.; Sarin, Rajiv; Scarpa, Aldo; van de Vijver, Marc; Futreal, P. Andrew; Aburatani, Hiroyuki; Bayés, Mónica; Bowtell, David D. L.; Campbell, Peter J.; Estivill, Xavier; Grimmond, Sean M.; Gut, Ivo; Hirst, Martin; López-Otín, Carlos; Majumder, Partha; Marra, Marco; McPherson, John D.; Ning, Zemin; Puente, Xose S.; Ruan, Yijun; Stunnenberg, Hendrik G.; Swerdlow, Harold; Velculescu, Victor E.; Wilson, Richard K.; Xue, Hong H.; Yang, Liu; Spellman, Paul T.; Bader, Gary D.; Boutros, Paul C.; Flicek, Paul; Getz, Gad; Guigó, Roderic; Guo, Guangwu; Haussler, David; Heath, Simon; Hubbard, Tim J.; Jiang, Tao; Jones, Steven M.; Li, Qibin; López-Bigas, Nuria; Luo, Ruibang; Muthuswamy, Lakshmi; Ouellette, B. F. Francis; Pearson, John V.; Quesada, Victor; Raphael, Benjamin J.; Sander, Chris; Speed, Terence P.; Stein, Lincoln D.; Stuart, Joshua M.; Teague, Jon W.; Totoki, Yasushi; Tsunoda, Tatsuhiko; Valencia, Alfonso; Wheeler, David A.; Wu, Honglong; Zhao, Shancen; Zhou, Guangyu; Lathrop, Mark; Thomas, Gilles; Yoshida, Teruhiko; Axton, Myles; Gunter, Chris; Miller, Linda J.; Zhang, Junjun; Haider, Syed A.; Wang, Jianxin; Yung, Christina K.; Cross, Anthony; Liang, Yong; Gnaneshan, Saravanamuttu; Guberman, Jonathan; Hsu, Jack; Chalmers, Don R. C.; Hasel, Karl W.; Kaan, Terry S. H.; Lowrance, William W.; Masui, Tohru; Rodriguez, Laura Lyman; Vergely, Catherine; Cloonan, Nicole; Defazio, Anna; Eshleman, James R.; Etemadmoghadam, Dariush; Gardiner, Brooke A.; Kench, James G.; Sutherland, Robert L.; Tempero, Margaret A.; Waddell, Nicola J.; Wilson, Peter J.; Gallinger, Steve; Tsao, Ming-Sound; Shaw, Patricia A.; Petersen, Gloria M.; Mukhopadhyay, Debabrata; DePinho, Ronald A.; Thayer, Sarah; Shazand, Kamran; Beck, Timothy; Sam, Michelle; Timms, Lee; Ballin, Vanessa; Ji, Jiafu; Zhang, Xiuqing; Chen, Feng; Hu, Xueda; Yang, Qi; Tian, Geng; Zhang, Lianhai; Xing, Xiaofang; Li, Xianghong; Zhu, Zhenggang; Yu, Yingyan; Yu, Jun; Tost, Jörg; Brennan, Paul; Holcatova, Ivana; Zaridze, David; Brazma, Alvis; Egevad, Lars; Prokhortchouk, Egor; Banks, Rosamonde Elizabeth; Uhlén, Mathias; Viksna, Juris; Ponten, Fredrik; Skryabin, Konstantin; Birney, Ewan; Borg, Ake; Børresen-Dale, Anne-Lise; Caldas, Carlos; Foekens, John A.; Martin, Sancha; Reis-Filho, Jorge S.; Richardson, Andrea L.; Sotiriou, Christos; van't Veer, Laura; Birnbaum, Daniel; Blanche, Hélène; Boucher, Pascal; Boyault, Sandrine; Masson-Jacquemier, Jocelyne D.; Pauporté, Iris; Pivot, Xavier; Vincent-Salomon, Anne; Tabone, Eric; Theillet, Charles; Treilleux, Isabelle; Bioulac-Sage, Paulette; Decaens, Thomas; Franco, Dominique; Gut, Marta; Samuel, Didier; Zucman-Rossi, Jessica; Eils, Roland; Brors, Benedikt; Korbel, Jan O.; Korshunov, Andrey; Landgraf, Pablo; Lehrach, Hans; Pfister, Stefan; Radlwimmer, Bernhard; Reifenberger, Guido; Taylor, Michael D.; von Kalle, Christof; Majumder, Partha P.; Pederzoli, Paolo; Lawlor, Rita T.; Delledonne, Massimo; Bardelli, Alberto; Gress, Thomas; Klimstra, David; Zamboni, Giuseppe; Nakamura, Yusuke; Miyano, Satoru; Fujimoto, Akihiro; Campo, Elias; de Sanjosé, Silvia; Montserrat, Emili; González-Díaz, Marcos; Jares, Pedro; Himmelbaue, Heinz; Bea, Silvia; Aparicio, Samuel; Easton, Douglas F.; Collins, Francis S.; Compton, Carolyn C.; Lander, Eric S.; Burke, Wylie; Green, Anthony R.; Hamilton, Stanley R.; Kallioniemi, Olli P.; Ley, Timothy J.; Liu, Edison T.; Wainwright, Brandon J.

    2010-01-01

    The International Cancer Genome Consortium (ICGC) was launched to coordinate large-scale cancer genome studies in tumours from 50 different cancer types and/or subtypes that are of clinical and societal importance across the globe. Systematic studies of more than 25,000 cancer genomes at the

  4. Genomic management of animal genetic diversity

    NARCIS (Netherlands)

    Oldenbroek, Kor

    2017-01-01

    Recently developed genomic tools, like SNP-genotyping and whole genome sequencing, and their analysis, offer great opportunities for the conservation and utilisation of animal genetic diversity, both among and within breeds. These genomic tools can be used to detect potentially valuable rare alleles

  5. The UCSC Genome Browser Database: update 2006

    DEFF Research Database (Denmark)

    Hinrichs, A S; Karolchik, D; Baertsch, R

    2006-01-01

    The University of California Santa Cruz Genome Browser Database (GBD) contains sequence and annotation data for the genomes of about a dozen vertebrate species and several major model organisms. Genome annotations typically include assembly data, sequence composition, genes and gene predictions, ...

  6. Intron size and genome size in plants.

    Science.gov (United States)

    J. Wendel; R. Cronn; I. Alvarez; B. Liu; R. Small; D. Senchina

    2002-01-01

    It has long been known that genomes vary over a remarkable range of sizes in both plants (Bennett, Cox, and Leitch 1997) and animals (Gregory 2001). It also has become evident that across the broad phylogenetic sweep, genome size may be correlated with intron size (Deutsch and Long 1999; Vinogradov 1999; McLysaght et al. 2000), suggesting that some component of genome...

  7. Leaner and meaner genomes in Escherichia coli

    DEFF Research Database (Denmark)

    Ussery, David

    2006-01-01

    A 'better' Escherichia coli K-12 genome has recently been engineered in which about 15% of the genome has been removed by planned deletions. Comparison with related bacterial genomes that have undergone a natural reduction in size suggests that there is plenty of scope for yet more deletions....

  8. Accounting for discovery bias in genomic EPD

    Science.gov (United States)

    Genomics has contributed substantially to genetic improvement of beef cattle. The implementation is through computation of genomically enhanced expected progeny differences (GE-EPD), which are predictions of genetic merit of individual animals based on genomic information, pedigree, and data on the ...

  9. Complete sequence of the mitochondrial genome of ...

    Indian Academy of Sciences (India)

    Supplementary data: Complete sequence of the mitochondrial genome of Odontamblyopus rubicundus (Perciformes: Gobiidae): genome characterization and phylogenetic analysis. Tianxing Liu, Xiaoxiao Jin, Rixin Wang and Tianjun Xu. J. Genet. 92, 423–432. Figure 1. Gene map of O. rubicundus mitochondrial genome.

  10. Impact of genomics on microbial food safety

    NARCIS (Netherlands)

    Abee, T.; Schaik, van W.; Siezen, R.J.

    2004-01-01

    Genome sequences are now available for many of the microbes that cause food-borne diseases. The information contained in pathogen genome sequences, together with the development of themed and whole-genome DNA microarrays and improved proteomics techniques, might provide tools for the rapid detection

  11. Overcoming Barriers to Progress in Exercise Genomics

    Science.gov (United States)

    Bouchard, Claude

    2011-01-01

    This commentary focuses on the issues of statistical power, the usefulness of hypothesis-free approaches such as in genome-wide association explorations, the necessity of expanding the research beyond common DNA variants, the advantage of combining transcriptomics with genomics, and the complexities inherent to the search for links between genotype and phenotype in exercise genomics research. PMID:21697717

  12. Comparative Genome Analysis in the Integrated Microbial Genomes(IMG) System

    Energy Technology Data Exchange (ETDEWEB)

    Kyrpides, Nikos C.; Markowitz, Victor M.

    2006-03-01

    Comparative genome analysis is critical for the effectiveexploration of a rapidly growing number of complete and draft sequencesfor microbial genomes. The Integrated Microbial Genomes (IMG) system(img.jgi.doe.gov) has been developed as a community resource thatprovides support for comparative analysis of microbial genomes in anintegrated context. IMG allows users to navigate the multidimensionalmicrobial genome data space and focus their analysis on a subset ofgenes, genomes, and functions of interest. IMG provides graphicalviewers, summaries and occurrence profile tools for comparing genes,pathways and functions (terms) across specific genomes. Genes can befurther examined using gene neighborhoods and compared with sequencealignment tools.

  13. Personal genomes in progress: from the human genome project to the personal genome project.

    Science.gov (United States)

    Lunshof, Jeantine E; Bobe, Jason; Aach, John; Angrist, Misha; Thakuria, Joseph V; Vorhaus, Daniel B; Hoehe, Margret R; Church, George M

    2010-01-01

    The cost of a diploid human genome sequence has dropped from about $70M to $2000 since 2007--even as the standards for redundancy have increased from 7x to 40x in order to improve call rates. Coupled with the low return on investment for common single-nucleotide polylmorphisms, this has caused a significant rise in interest in correlating genome sequences with comprehensive environmental and trait data (GET). The cost of electronic health records, imaging, and microbial, immunological, and behavioral data are also dropping quickly. Sharing such integrated GET datasets and their interpretations with a diversity of researchers and research subjects highlights the need for informed-consent models capable of addressing novel privacy and other issues, as well as for flexible data-sharing resources that make materials and data available with minimum restrictions on use. This article examines the Personal Genome Project's effort to develop a GET database as a public genomics resource broadly accessible to both researchers and research participants, while pursuing the highest standards in research ethics.

  14. Biosurveillance enterprise for operational awareness, a genomic-based approach for tracking pathogen virulence.

    Science.gov (United States)

    Valdivia-Granda, Willy A

    2013-11-15

    To protect our civilians and warfighters against both known and unknown pathogens, biodefense stakeholders must be able to foresee possible technological trends that could affect their threat risk assessment. However, significant flaws in how we prioritize our countermeasure-needs continue to limit their development. As recombinant biotechnology becomes increasingly simplified and inexpensive, small groups, and even individuals, can now achieve the design, synthesis, and production of pathogenic organisms for offensive purposes. Under these daunting circumstances, a reliable biosurveillance approach that supports a diversity of users could better provide early warnings about the emergence of new pathogens (both natural and manmade), reverse engineer pathogens carrying traits to avoid available countermeasures, and suggest the most appropriate detection, prophylactic, and therapeutic solutions. While impressive in data mining capabilities, real-time content analysis of social media data misses much of the complexity in the factual reality. Quality issues within freeform user-provided hashtags and biased referencing can significantly undermine our confidence in the information obtained to make critical decisions about the natural vs. intentional emergence of a pathogen. At the same time, errors in pathogen genomic records, the narrow scope of most databases, and the lack of standards and interoperability across different detection and diagnostic devices, continue to restrict the multidimensional biothreat assessment. The fragmentation of our biosurveillance efforts into different approaches has stultified attempts to implement any new foundational enterprise that is more reliable, more realistic and that avoids the scenario of the warning that comes too late. This discussion focus on the development of genomic-based decentralized medical intelligence and laboratory system to track emerging and novel microbial health threats in both military and civilian settings and

  15. Public health genomics: origins and basic concepts

    Directory of Open Access Journals (Sweden)

    Ron Zimmern

    2006-12-01

    Full Text Available Knowledge and technologies arising from the Human Genome Project promise in time to offer new opportunities for the treatment and prevention of disease. The enterprise of public health genomics aims to bridge the gap between advances in basic research and their responsible and effective implementation in clinical services and public health programmes. Public health genomics stresses the importance of understanding how genes and environment act together to influence health; avoiding genetic exceptionalism; appreciating the social and political context of genomic advances; and encouraging critical evaluation of proposed new tests and interventions. New international networks and collaborations are being established to develop public health genomics and further its aims.

  16. Comparison of 61 Sequenced Escherichia coli Genomes

    DEFF Research Database (Denmark)

    Lukjancenko, Oksana; Wassenaar, T. M.; Ussery, David

    2010-01-01

    Escherichia coli is an important component of the biosphere and is an ideal model for studies of processes involved in bacterial genome evolution. Sixty-one publically available E. coli and Shigella spp. sequenced genomes are compared, using basic methods to produce phylogenetic and proteomics......% of the pan-genome and about 80% of a typical genome; some of these variable genes tend to be co-localized on genomic islands. The diversity within the species E. coli, and the overlap in gene content between this and related species, suggests a continuum rather than sharp species borders in this group...

  17. Prospects for Genomic Research in Forestry

    Directory of Open Access Journals (Sweden)

    K. V. Krutovsky

    2014-08-01

    Full Text Available Conifers are keystone species of boreal forests. Their whole genome sequencing, assembly and annotation will allow us to understand the evolution of the complex ancient giant conifer genomes that are 4 times larger in larch and 7–9 times larger in pines than the human genome. Genomic studies will allow also to obtain important whole genome sequence data and develop highly polymorphic and informative genetic markers, such as microsatellites and single nucleotide polymorphisms (SNPs that can be efficiently used in timber origin identification, for genetic variation monitoring, to study local and climate change adaptation and in tree improvement and conservation programs.

  18. Software for computing and annotating genomic ranges.

    Science.gov (United States)

    Lawrence, Michael; Huber, Wolfgang; Pagès, Hervé; Aboyoun, Patrick; Carlson, Marc; Gentleman, Robert; Morgan, Martin T; Carey, Vincent J

    2013-01-01

    We describe Bioconductor infrastructure for representing and computing on annotated genomic ranges and integrating genomic data with the statistical computing features of R and its extensions. At the core of the infrastructure are three packages: IRanges, GenomicRanges, and GenomicFeatures. These packages provide scalable data structures for representing annotated ranges on the genome, with special support for transcript structures, read alignments and coverage vectors. Computational facilities include efficient algorithms for overlap and nearest neighbor detection, coverage calculation and other range operations. This infrastructure directly supports more than 80 other Bioconductor packages, including those for sequence analysis, differential expression analysis and visualization.

  19. Software for computing and annotating genomic ranges.

    Directory of Open Access Journals (Sweden)

    Michael Lawrence

    Full Text Available We describe Bioconductor infrastructure for representing and computing on annotated genomic ranges and integrating genomic data with the statistical computing features of R and its extensions. At the core of the infrastructure are three packages: IRanges, GenomicRanges, and GenomicFeatures. These packages provide scalable data structures for representing annotated ranges on the genome, with special support for transcript structures, read alignments and coverage vectors. Computational facilities include efficient algorithms for overlap and nearest neighbor detection, coverage calculation and other range operations. This infrastructure directly supports more than 80 other Bioconductor packages, including those for sequence analysis, differential expression analysis and visualization.

  20. The ecoresponsive genome of Daphnia pulex

    Energy Technology Data Exchange (ETDEWEB)

    Colbourne, John K.; Pfrender, Michael E.; Gilbert, Donald; Thomas, W. Kelley; Tucker, Abraham; Oakley, Todd H.; Tokishita, Shinichi; Aerts, Andrea; Arnold, Georg J.; Basu, Malay Kumar; Bauer, Darren J.; Caceres, Carla E.; Carmel, Liran; Casola, Claudio; Choi, Jeong-Hyeon; Detter, John C.; Dong, Qunfeng; Dusheyko, Serge; Eads, Brian D.; Frohlich, Thomas; Geiler-Samerotte, Kerry A.; Gerlach, Daniel; Hatcher, Phil; Jogdeo, Sanjuro; Krijgsveld, Jeroen; Kriventseva, Evgenia V; Kültz, Dietmar; Laforsch, Christian; Lindquist, Erika; Lopez, Jacqueline; Manak, Robert; Muller, Jean; Pangilinan, Jasmyn; Patwardhan, Rupali P.; Pitluck, Samuel; Pritham, Ellen J.; Rechtsteiner, Andreas; Rho, Mina; Rogozin, Igor B.; Sakarya, Onur; Salamov, Asaf; Schaack, Sarah; Shapiro, Harris; Shiga, Yasuhiro; Skalitzky, Courtney; Smith, Zachary; Souvorov, Alexander; Sung, Way; Tang, Zuojian; Tsuchiya, Dai; Tu, Hank; Vos, Harmjan; Wang, Mei; Wolf, Yuri I.; Yamagata, Hideo; Yamada, Takuji; Ye, Yuzhen; Shaw, Joseph R.; Andrews, Justen; Crease, Teresa J.; Tang, Haixu; Lucas, Susan M.; Robertson, Hugh M.; Bork, Peer; Koonin, Eugene V.; Zdobnov, Evgeny M.; Grigoriev, Igor V.; Lynch, Michael; Boore, Jeffrey L.

    2011-02-04

    This document provides supporting material related to the sequencing of the ecoresponsive genome of Daphnia pulex. This material includes information on materials and methods and supporting text, as well as supplemental figures, tables, and references. The coverage of materials and methods addresses genome sequence, assembly, and mapping to chromosomes, gene inventory, attributes of a compact genome, the origin and preservation of Daphnia pulex genes, implications of Daphnia's genome structure, evolutionary diversification of duplicated genes, functional significance of expanded gene families, and ecoresponsive genes. Supporting text covers chromosome studies, gene homology among Daphnia genomes, micro-RNA and transposable elements and the 46 Daphnia pulex opsins. 36 figures, 50 tables, 183 references.